├── .gitignore ├── ChangeLog ├── Library └── libStatGenForMinimac3 │ ├── Doxyfile │ ├── Makefile │ ├── Makefiles │ ├── Makefile.base │ ├── Makefile.common │ ├── Makefile.ext │ ├── Makefile.extlib │ ├── Makefile.footer │ ├── Makefile.help │ ├── Makefile.include │ ├── Makefile.lib │ ├── Makefile.src │ ├── Makefile.test │ ├── Makefile.tool │ ├── Makefile.toolchain │ └── Makefile.wholepackage │ ├── README.md │ ├── README.txt │ ├── bam │ ├── BamIndex.cpp │ ├── BamIndex.h │ ├── BamInterface.cpp │ ├── BamInterface.h │ ├── COPYING │ ├── CigarHelper.cpp │ ├── CigarHelper.h │ ├── GenericSamInterface.cpp │ ├── GenericSamInterface.h │ ├── Makefile │ ├── Makefile.depends │ ├── Pileup.h │ ├── PileupElement.cpp │ ├── PileupElement.h │ ├── PileupElementBaseQual.cpp │ ├── PileupElementBaseQual.h │ ├── PosList.cpp │ ├── PosList.h │ ├── SamCoordOutput.cpp │ ├── SamCoordOutput.h │ ├── SamFile.cpp │ ├── SamFile.h │ ├── SamFileHeader.cpp │ ├── SamFileHeader.h │ ├── SamFilter.cpp │ ├── SamFilter.h │ ├── SamFlag.h │ ├── SamHeaderHD.cpp │ ├── SamHeaderHD.h │ ├── SamHeaderPG.cpp │ ├── SamHeaderPG.h │ ├── SamHeaderRG.cpp │ ├── SamHeaderRG.h │ ├── SamHeaderRecord.cpp │ ├── SamHeaderRecord.h │ ├── SamHeaderSQ.cpp │ ├── SamHeaderSQ.h │ ├── SamHeaderTag.cpp │ ├── SamHeaderTag.h │ ├── SamHelper.h │ ├── SamInterface.cpp │ ├── SamInterface.h │ ├── SamQuerySeqWithRefHelper.cpp │ ├── SamQuerySeqWithRefHelper.h │ ├── SamRecord.cpp │ ├── SamRecord.h │ ├── SamRecordHelper.cpp │ ├── SamRecordHelper.h │ ├── SamRecordPool.cpp │ ├── SamRecordPool.h │ ├── SamReferenceInfo.cpp │ ├── SamReferenceInfo.h │ ├── SamStatistics.cpp │ ├── SamStatistics.h │ ├── SamStatus.h │ ├── SamTags.cpp │ ├── SamTags.h │ ├── SamValidation.cpp │ ├── SamValidation.h │ ├── examples │ │ ├── Makefile │ │ ├── pileup │ │ │ ├── .gitignore │ │ │ ├── Main.cpp │ │ │ └── Makefile │ │ └── printRefPositions │ │ │ ├── .gitignore │ │ │ ├── Main.cpp │ │ │ ├── Makefile │ │ │ ├── PrintRefPositions.cpp │ │ │ ├── PrintRefPositions.h │ │ │ └── expected │ │ │ └── test.txt │ └── test │ │ ├── .gitignore │ │ ├── BamIndexTest.cpp │ │ ├── BamIndexTest.h │ │ ├── Main.cpp │ │ ├── Makefile │ │ ├── Modify.cpp │ │ ├── Modify.h │ │ ├── ModifyVar.cpp │ │ ├── ModifyVar.h │ │ ├── ReadFiles.cpp │ │ ├── ReadFiles.h │ │ ├── SamFileTest.cpp │ │ ├── SamFileTest.h │ │ ├── ShiftIndels.cpp │ │ ├── ShiftIndels.h │ │ ├── TestCigarHelper.cpp │ │ ├── TestCigarHelper.h │ │ ├── TestEquals.cpp │ │ ├── TestEquals.h │ │ ├── TestFilter.cpp │ │ ├── TestFilter.h │ │ ├── TestPileup.cpp │ │ ├── TestPileup.h │ │ ├── TestPosList.cpp │ │ ├── TestPosList.h │ │ ├── TestSamCoordOutput.cpp │ │ ├── TestSamCoordOutput.h │ │ ├── TestSamRecordHelper.cpp │ │ ├── TestSamRecordHelper.h │ │ ├── TestSamRecordPool.cpp │ │ ├── TestSamRecordPool.h │ │ ├── TestValidate.cpp │ │ ├── TestValidate.h │ │ ├── ValidationTest.cpp │ │ ├── ValidationTest.h │ │ ├── WriteFiles.cpp │ │ ├── WriteFiles.h │ │ ├── expected │ │ ├── TestSamCoordOutput.sam │ │ ├── addedTagToBam.bam │ │ ├── addedTagToBam.sam │ │ ├── addedTagToSam.bam │ │ ├── addedTagToSam.sam │ │ ├── noZlib │ │ │ ├── TestSamCoordOutput.sam │ │ │ ├── addedTagToBam.bam │ │ │ ├── addedTagToBam.sam │ │ │ ├── addedTagToSam.bam │ │ │ ├── addedTagToSam.sam │ │ │ ├── samTest.log │ │ │ ├── testEqWithBases.bam │ │ │ ├── testEqWithBases.sam │ │ │ ├── testEqWithEq.bam │ │ │ ├── testEqWithEq.sam │ │ │ ├── testEqWithOrig.bam │ │ │ ├── testEqWithOrig.sam │ │ │ ├── testShift.bam │ │ │ ├── testShift.sam │ │ │ ├── updateTag.bam │ │ │ ├── updateTagFromBam.sam │ │ │ └── updateTagFromSam.sam │ │ ├── samTest.log │ │ ├── testEqWithBases.bam │ │ ├── testEqWithBases.sam │ │ ├── testEqWithEq.bam │ │ ├── testEqWithEq.sam │ │ ├── testEqWithOrig.bam │ │ ├── testEqWithOrig.sam │ │ ├── testShift.bam │ │ ├── testShift.sam │ │ ├── updateTag.bam │ │ ├── updateTagFromBam.sam │ │ └── updateTagFromSam.sam │ │ ├── results │ │ └── .gitignore │ │ ├── test.sh │ │ └── testFiles │ │ ├── chr1_partial-bs.umfa │ │ ├── chr1_partial.fa │ │ ├── sortedBam.bam │ │ ├── sortedBam.bam.bai │ │ ├── sortedBam2.bai │ │ ├── sortedBam2.bam │ │ ├── testBam.bam │ │ ├── testBam1.bam │ │ ├── testEq.bam │ │ ├── testEq.sam │ │ ├── testSam.sam │ │ ├── testSam1.sam │ │ ├── testSamSOcoord.sam │ │ ├── testSamSOinvalid.sam │ │ ├── testSamSOquery.sam │ │ ├── testShift.bam │ │ ├── testShift.sam │ │ └── testVar.bam │ ├── copyrights │ ├── COPYING │ ├── COPYING.samtools │ ├── LICENSE.md5 │ ├── LICENSE.twister │ └── LICENSE.txt │ ├── fastq │ ├── BaseComposition.cpp │ ├── BaseComposition.h │ ├── BaseCount.cpp │ ├── BaseCount.h │ ├── COPYING │ ├── FastQFile.cpp │ ├── FastQFile.h │ ├── FastQStatus.cpp │ ├── FastQStatus.h │ ├── Makefile │ ├── Makefile.depends │ └── test │ │ ├── .gitignore │ │ ├── FastQFileTest.cpp │ │ ├── FastQValidatorTest.sh │ │ ├── Makefile │ │ ├── README.txt │ │ ├── expectedResults │ │ └── ExpectedResultsFastqTestResults.txt │ │ └── testFile.txt │ ├── general │ ├── BaseAsciiMap.cpp │ ├── BaseAsciiMap.h │ ├── BaseQualityHelper.cpp │ ├── BaseQualityHelper.h │ ├── BaseUtilities.cpp │ ├── BaseUtilities.h │ ├── BasicHash.cpp │ ├── BasicHash.h │ ├── BgzfFileType.cpp │ ├── BgzfFileType.h │ ├── BgzfFileTypeRecovery.cpp │ ├── BgzfFileTypeRecovery.h │ ├── CSG_MD5.h │ ├── CharBuffer.cpp │ ├── CharBuffer.h │ ├── Chromosome.cpp │ ├── Chromosome.h │ ├── Cigar.cpp │ ├── Cigar.h │ ├── CigarRoller.cpp │ ├── CigarRoller.h │ ├── Constant.h │ ├── Error.cpp │ ├── Error.h │ ├── ErrorHandler.cpp │ ├── ErrorHandler.h │ ├── FileType.cpp │ ├── FileType.h │ ├── FortranFormat.cpp │ ├── FortranFormat.h │ ├── Generic.cpp │ ├── Generic.h │ ├── GenomeSequence.cpp │ ├── GenomeSequence.h │ ├── GenomeSequenceHelpers.h │ ├── GenotypeLists.cpp │ ├── GenotypeLists.h │ ├── GreedyTupleAligner.h │ ├── GzipFileType.cpp │ ├── GzipFileType.h │ ├── GzipHeader.cpp │ ├── GzipHeader.h │ ├── Hash.cpp │ ├── Hash.h │ ├── IndexBase.cpp │ ├── IndexBase.h │ ├── InplaceMerge.cpp │ ├── InplaceMerge.h │ ├── Input.cpp │ ├── Input.h │ ├── InputFile.cpp │ ├── InputFile.h │ ├── IntArray.cpp │ ├── IntArray.h │ ├── IntHash.cpp │ ├── IntHash.h │ ├── LICENSE.twister │ ├── LICENSE.txt │ ├── LongHash.h │ ├── LongInt.h │ ├── LongLongCounter.cpp │ ├── LongLongCounter.h │ ├── Makefile │ ├── Makefile.depends │ ├── MapFunction.cpp │ ├── MapFunction.h │ ├── MathConstant.h │ ├── MathMatrix.cpp │ ├── MathMatrix.h │ ├── MathVector.cpp │ ├── MathVector.h │ ├── MemoryAllocators.cpp │ ├── MemoryAllocators.h │ ├── MemoryInfo.cpp │ ├── MemoryInfo.h │ ├── MemoryMap.cpp │ ├── MemoryMap.h │ ├── MemoryMapArray.cpp │ ├── MemoryMapArray.h │ ├── MiniDeflate.cpp │ ├── MiniDeflate.h │ ├── NonOverlapRegions.cpp │ ├── NonOverlapRegions.h │ ├── PackedVector.h │ ├── Parameters.cpp │ ├── Parameters.h │ ├── Pedigree.cpp │ ├── Pedigree.h │ ├── PedigreeAlleleFreq.cpp │ ├── PedigreeAlleleFreq.h │ ├── PedigreeAlleles.h │ ├── PedigreeDescription.cpp │ ├── PedigreeDescription.h │ ├── PedigreeFamily.cpp │ ├── PedigreeFamily.h │ ├── PedigreeGlobals.cpp │ ├── PedigreeGlobals.h │ ├── PedigreeLoader.cpp │ ├── PedigreePerson.cpp │ ├── PedigreePerson.h │ ├── PedigreeTrim.cpp │ ├── PedigreeTwin.cpp │ ├── Performance.h │ ├── PhoneHome.cpp │ ├── PhoneHome.h │ ├── QuickIndex.cpp │ ├── QuickIndex.h │ ├── Random.cpp │ ├── Random.h │ ├── ReferenceSequence.cpp │ ├── ReferenceSequence.h │ ├── ReusableVector.h │ ├── STLUtilities.cpp │ ├── STLUtilities.h │ ├── SimpleStats.h │ ├── SmithWaterman.cpp │ ├── SmithWaterman.h │ ├── Sort.cpp │ ├── Sort.h │ ├── StatGenStatus.cpp │ ├── StatGenStatus.h │ ├── String.cpp │ ├── StringAlias.cpp │ ├── StringAlias.h │ ├── StringArray.cpp │ ├── StringArray.h │ ├── StringBasics.cpp │ ├── StringBasics.h │ ├── StringHash.cpp │ ├── StringHash.h │ ├── StringMap.cpp │ ├── StringMap.h │ ├── Tabix.cpp │ ├── Tabix.h │ ├── TrimSequence.h │ ├── UncompressedFileType.cpp │ ├── UncompressedFileType.h │ ├── UnitTest.h │ ├── glfHandler.cpp │ ├── glfHandler.h │ └── test │ │ ├── Chromosome_test.cpp │ │ ├── GenomeSequence_test.cpp │ │ ├── GreedyTupleAligner_test.cpp │ │ ├── Makefile │ │ ├── STLUtilities_test.cpp │ │ ├── TrimSequence_test.cpp │ │ ├── baseUtilitiesTest │ │ ├── .gitignore │ │ ├── BaseUtilitiesTest.cpp │ │ ├── BaseUtilitiesTest.h │ │ └── Makefile │ │ ├── cigar │ │ ├── .gitignore │ │ ├── CigarRollerTest.cpp │ │ ├── CigarRollerTest.h │ │ └── Makefile │ │ ├── dbsnp │ │ ├── .gitignore │ │ ├── Main.cpp │ │ ├── Makefile │ │ ├── expected │ │ │ └── results.txt │ │ └── testFiles │ │ │ ├── chr1_partial-bs.umfa │ │ │ ├── chr1_partial.fa │ │ │ ├── dbsnp.vcf │ │ │ └── dbsnp.vcf.gz │ │ ├── gtest.cpp │ │ ├── inputFileTest │ │ ├── .gitignore │ │ ├── InputFileTest.cpp │ │ ├── InputFileTest.h │ │ ├── Makefile │ │ ├── data │ │ │ ├── InputFileTest.bam │ │ │ ├── InputFileTest.glf │ │ │ ├── InputFileTest.gz │ │ │ ├── InputFileTest.txt │ │ │ ├── InputFileTest2.gz │ │ │ ├── InputFileTest2.txt │ │ │ ├── InputFileTestLarge.bam │ │ │ ├── InputFileTestLarge.glf │ │ │ ├── InputFileTestLarge.gz │ │ │ ├── InputFileTestLarge.txt │ │ │ ├── textFile.gz │ │ │ └── textFile.txt │ │ └── expected │ │ │ ├── results.log │ │ │ └── resultsNoZlib.log │ │ ├── memoryMapArrayTest │ │ ├── .gitignore │ │ ├── Makefile │ │ ├── MemoryMapArrayTest.cpp │ │ └── MemoryMapArrayTest.h │ │ ├── nonOverlapRegions │ │ ├── .gitignore │ │ ├── Makefile │ │ ├── NonOverlapRegionsTest.cpp │ │ ├── NonOverlapRegionsTest.h │ │ ├── expectedNonOverlapRegionsTest.txt │ │ └── results │ │ │ └── .gitignore │ │ ├── packedVectorTest │ │ ├── .gitignore │ │ ├── Makefile │ │ ├── PackedVectorTest.cpp │ │ └── PackedVectorTest.h │ │ ├── phiX.fa │ │ ├── referenceSequenceTest │ │ ├── .gitignore │ │ ├── Makefile │ │ ├── ReferenceSequenceTest.cpp │ │ └── ReferenceSequenceTest.h │ │ ├── reusableVector │ │ ├── .gitignore │ │ ├── Makefile │ │ ├── ReusableVectorTest.cpp │ │ └── ReusableVectorTest.h │ │ ├── string │ │ ├── .gitignore │ │ ├── Makefile │ │ ├── StringTest.cpp │ │ ├── StringTest.h │ │ └── testFiles │ │ │ └── testFile.txt │ │ ├── test_memmap_data.txt │ │ └── trimSequence │ │ ├── .gitignore │ │ ├── Makefile │ │ └── TrimSequence.cpp │ ├── glf │ ├── COPYING │ ├── GlfException.cpp │ ├── GlfException.h │ ├── GlfFile.cpp │ ├── GlfFile.h │ ├── GlfHeader.cpp │ ├── GlfHeader.h │ ├── GlfRecord.cpp │ ├── GlfRecord.h │ ├── GlfRefSection.cpp │ ├── GlfRefSection.h │ ├── GlfStatus.cpp │ ├── GlfStatus.h │ ├── Makefile │ ├── Makefile.depends │ └── test │ │ ├── .gitignore │ │ ├── Main.cpp │ │ ├── Makefile │ │ ├── ReadFiles.cpp │ │ ├── ReadFiles.h │ │ ├── Validate.cpp │ │ ├── Validate.h │ │ ├── WriteFiles.cpp │ │ ├── WriteFiles.h │ │ ├── results │ │ └── .gitignore │ │ └── testFiles │ │ └── testGlf.glf │ ├── include │ └── .gitignore │ ├── samtools │ ├── COPYING │ ├── Makefile │ ├── Makefile.depends │ ├── README.txt │ ├── bam.h │ ├── bgzf.c │ ├── bgzf.h │ ├── khash.h │ ├── knetfile.c │ └── knetfile.h │ └── vcf │ ├── Makefile │ ├── VcfFile.cpp │ ├── VcfFile.h │ ├── VcfFileReader.cpp │ ├── VcfFileReader.h │ ├── VcfFileWriter.cpp │ ├── VcfFileWriter.h │ ├── VcfGenotypeField.cpp │ ├── VcfGenotypeField.h │ ├── VcfGenotypeFormat.cpp │ ├── VcfGenotypeFormat.h │ ├── VcfGenotypeSample.cpp │ ├── VcfGenotypeSample.h │ ├── VcfHeader.cpp │ ├── VcfHeader.h │ ├── VcfHelper.cpp │ ├── VcfHelper.h │ ├── VcfRecord.cpp │ ├── VcfRecord.h │ ├── VcfRecordDiscardRules.cpp │ ├── VcfRecordDiscardRules.h │ ├── VcfRecordField.cpp │ ├── VcfRecordField.h │ ├── VcfRecordFilter.cpp │ ├── VcfRecordFilter.h │ ├── VcfRecordGenotype.cpp │ ├── VcfRecordGenotype.h │ ├── VcfRecordInfo.cpp │ ├── VcfRecordInfo.h │ ├── VcfSubsetSamples.cpp │ ├── VcfSubsetSamples.h │ └── test │ ├── .gitignore │ ├── Main.cpp │ ├── Makefile │ ├── VcfFileTest.cpp │ ├── VcfFileTest.h │ ├── VcfHeaderTest.cpp │ ├── VcfHeaderTest.h │ ├── expected │ ├── vcfFileNoInfo.vcf │ ├── vcfFileNoInfoBGZF.vcf │ ├── vcfFileNoInfoKeepGQHQ.vcf │ ├── vcfFileNoInfoKeepGT.vcf │ └── vcfHeader.vcf │ ├── results │ └── .gitignore │ └── testFiles │ ├── exclude2.txt │ ├── excludeIDs.txt │ ├── includeIDs.txt │ ├── subset1.txt │ ├── subset2.txt │ ├── testTabix.vcf │ ├── testTabix.vcf.bgzf │ ├── testTabix.vcf.bgzf.tbi │ ├── testTabixBadIndex.vcf.bgzf │ ├── testTabixBadIndex.vcf.bgzf.tbi │ └── vcfFile.vcf ├── Makefile ├── Makefile.inc ├── README.txt ├── copyrights ├── COPYING └── LICENSE.txt ├── src ├── HaplotypeSet.cpp ├── HaplotypeSet.h ├── Imputation.cpp ├── Imputation.h ├── ImputationStatistics.cpp ├── ImputationStatistics.h ├── Main.cpp ├── Makefile ├── MarkovModel.cpp ├── MarkovModel.h ├── MarkovParameters.cpp ├── MarkovParameters.h ├── Unique.cpp └── Unique.h └── test ├── refPanel.m3vcf.gz ├── refPanel.vcf ├── refPanel.vcf.gz ├── refPanelChrX.Non.Auto.vcf ├── sample.txt.filepart ├── targetStudy.vcf ├── targetStudyChrX.females.vcf └── targetStudyChrX.males.vcf /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/.gitignore -------------------------------------------------------------------------------- /ChangeLog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/ChangeLog -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Doxyfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Doxyfile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefiles/Makefile.base: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefiles/Makefile.base -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefiles/Makefile.common: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefiles/Makefile.common -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefiles/Makefile.ext: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefiles/Makefile.ext -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefiles/Makefile.extlib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefiles/Makefile.extlib -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefiles/Makefile.footer: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefiles/Makefile.footer -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefiles/Makefile.help: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefiles/Makefile.help -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefiles/Makefile.include: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefiles/Makefile.include -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefiles/Makefile.lib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefiles/Makefile.lib -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefiles/Makefile.src: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefiles/Makefile.src -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefiles/Makefile.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefiles/Makefile.test -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefiles/Makefile.tool: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefiles/Makefile.tool -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefiles/Makefile.toolchain: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefiles/Makefile.toolchain -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/Makefiles/Makefile.wholepackage: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/Makefiles/Makefile.wholepackage -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/README.md -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/README.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/BamIndex.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/BamIndex.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/BamIndex.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/BamIndex.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/BamInterface.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/BamInterface.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/BamInterface.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/BamInterface.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/COPYING: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/COPYING -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/CigarHelper.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/CigarHelper.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/CigarHelper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/CigarHelper.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/GenericSamInterface.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/GenericSamInterface.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/GenericSamInterface.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/GenericSamInterface.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/Makefile.depends: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/Makefile.depends -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/Pileup.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/Pileup.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/PileupElement.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/PileupElement.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/PileupElement.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/PileupElement.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/PileupElementBaseQual.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/PileupElementBaseQual.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/PileupElementBaseQual.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/PileupElementBaseQual.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/PosList.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/PosList.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/PosList.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/PosList.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamCoordOutput.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamCoordOutput.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamCoordOutput.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamCoordOutput.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamFile.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamFile.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamFile.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamFile.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamFileHeader.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamFileHeader.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamFileHeader.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamFileHeader.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamFilter.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamFilter.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamFilter.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamFilter.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamFlag.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamFlag.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamHeaderHD.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamHeaderHD.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamHeaderHD.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamHeaderHD.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamHeaderPG.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamHeaderPG.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamHeaderPG.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamHeaderPG.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamHeaderRG.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamHeaderRG.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamHeaderRG.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamHeaderRG.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamHeaderRecord.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamHeaderRecord.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamHeaderRecord.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamHeaderRecord.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamHeaderSQ.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamHeaderSQ.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamHeaderSQ.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamHeaderSQ.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamHeaderTag.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamHeaderTag.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamHeaderTag.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamHeaderTag.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamHelper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamHelper.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamInterface.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamInterface.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamInterface.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamInterface.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamQuerySeqWithRefHelper.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamQuerySeqWithRefHelper.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamQuerySeqWithRefHelper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamQuerySeqWithRefHelper.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamRecord.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamRecord.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamRecord.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamRecord.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamRecordHelper.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamRecordHelper.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamRecordHelper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamRecordHelper.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamRecordPool.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamRecordPool.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamRecordPool.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamRecordPool.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamReferenceInfo.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamReferenceInfo.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamReferenceInfo.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamReferenceInfo.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamStatistics.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamStatistics.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamStatistics.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamStatistics.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamStatus.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamStatus.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamTags.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamTags.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamTags.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamTags.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamValidation.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamValidation.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/SamValidation.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/SamValidation.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/examples/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/examples/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/examples/pileup/.gitignore: -------------------------------------------------------------------------------- 1 | pileup 2 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/examples/pileup/Main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/examples/pileup/Main.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/examples/pileup/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/examples/pileup/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/examples/printRefPositions/.gitignore: -------------------------------------------------------------------------------- 1 | printRefPositions 2 | results/ -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/examples/printRefPositions/Main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/examples/printRefPositions/Main.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/examples/printRefPositions/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/examples/printRefPositions/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/examples/printRefPositions/PrintRefPositions.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/examples/printRefPositions/PrintRefPositions.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/examples/printRefPositions/PrintRefPositions.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/examples/printRefPositions/PrintRefPositions.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/examples/printRefPositions/expected/test.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/examples/printRefPositions/expected/test.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/.gitignore: -------------------------------------------------------------------------------- 1 | samTest 2 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/BamIndexTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/BamIndexTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/BamIndexTest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/BamIndexTest.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/Main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/Main.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/Modify.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/Modify.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/Modify.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/Modify.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/ModifyVar.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/ModifyVar.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/ModifyVar.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/ModifyVar.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/ReadFiles.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/ReadFiles.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/ReadFiles.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/ReadFiles.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/SamFileTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/SamFileTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/SamFileTest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/SamFileTest.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/ShiftIndels.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/ShiftIndels.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/ShiftIndels.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/ShiftIndels.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestCigarHelper.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestCigarHelper.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestCigarHelper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestCigarHelper.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestEquals.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestEquals.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestEquals.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestEquals.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestFilter.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestFilter.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestFilter.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestFilter.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestPileup.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestPileup.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestPileup.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestPileup.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestPosList.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestPosList.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestPosList.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestPosList.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestSamCoordOutput.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestSamCoordOutput.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestSamCoordOutput.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestSamCoordOutput.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestSamRecordHelper.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestSamRecordHelper.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestSamRecordHelper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestSamRecordHelper.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestSamRecordPool.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestSamRecordPool.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestSamRecordPool.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestSamRecordPool.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestValidate.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestValidate.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/TestValidate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/TestValidate.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/ValidationTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/ValidationTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/ValidationTest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/ValidationTest.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/WriteFiles.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/WriteFiles.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/WriteFiles.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/WriteFiles.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/TestSamCoordOutput.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/TestSamCoordOutput.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/addedTagToBam.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/addedTagToBam.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/addedTagToBam.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/addedTagToBam.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/addedTagToSam.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/addedTagToSam.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/addedTagToSam.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/addedTagToSam.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/TestSamCoordOutput.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/noZlib/TestSamCoordOutput.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/addedTagToBam.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/noZlib/addedTagToBam.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/addedTagToBam.sam: -------------------------------------------------------------------------------- 1 | ../addedTagToBam.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/addedTagToSam.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/noZlib/addedTagToSam.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/addedTagToSam.sam: -------------------------------------------------------------------------------- 1 | ../addedTagToSam.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/samTest.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/noZlib/samTest.log -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/testEqWithBases.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/noZlib/testEqWithBases.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/testEqWithBases.sam: -------------------------------------------------------------------------------- 1 | ../testEqWithBases.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/testEqWithEq.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/noZlib/testEqWithEq.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/testEqWithEq.sam: -------------------------------------------------------------------------------- 1 | ../testEqWithEq.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/testEqWithOrig.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/noZlib/testEqWithOrig.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/testEqWithOrig.sam: -------------------------------------------------------------------------------- 1 | ../testEqWithOrig.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/testShift.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/noZlib/testShift.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/testShift.sam: -------------------------------------------------------------------------------- 1 | ../testShift.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/updateTag.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/noZlib/updateTag.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/updateTagFromBam.sam: -------------------------------------------------------------------------------- 1 | ../updateTagFromBam.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/noZlib/updateTagFromSam.sam: -------------------------------------------------------------------------------- 1 | ../updateTagFromSam.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/samTest.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/samTest.log -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/testEqWithBases.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/testEqWithBases.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/testEqWithBases.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/testEqWithBases.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/testEqWithEq.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/testEqWithEq.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/testEqWithEq.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/testEqWithEq.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/testEqWithOrig.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/testEqWithOrig.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/testEqWithOrig.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/testEqWithOrig.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/testShift.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/testShift.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/testShift.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/testShift.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/updateTag.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/updateTag.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/updateTagFromBam.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/updateTagFromBam.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/expected/updateTagFromSam.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/expected/updateTagFromSam.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/results/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/results/.gitignore -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/test.sh -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/chr1_partial-bs.umfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/chr1_partial-bs.umfa -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/chr1_partial.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/chr1_partial.fa -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/sortedBam.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/sortedBam.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/sortedBam.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/sortedBam.bam.bai -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/sortedBam2.bai: -------------------------------------------------------------------------------- 1 | sortedBam.bam.bai -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/sortedBam2.bam: -------------------------------------------------------------------------------- 1 | sortedBam.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/testBam.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/testBam.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/testBam1.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/testBam1.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/testEq.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/testEq.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/testEq.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/testEq.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/testSam.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/testSam.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/testSam1.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/testSam1.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/testSamSOcoord.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/testSamSOcoord.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/testSamSOinvalid.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/testSamSOinvalid.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/testSamSOquery.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/testSamSOquery.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/testShift.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/testShift.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/testShift.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/testShift.sam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/bam/test/testFiles/testVar.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/bam/test/testFiles/testVar.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/copyrights/COPYING: -------------------------------------------------------------------------------- 1 | LICENSE.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/copyrights/COPYING.samtools: -------------------------------------------------------------------------------- 1 | ../samtools/COPYING -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/copyrights/LICENSE.md5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/copyrights/LICENSE.md5 -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/copyrights/LICENSE.twister: -------------------------------------------------------------------------------- 1 | ../general/LICENSE.twister -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/copyrights/LICENSE.txt: -------------------------------------------------------------------------------- 1 | ../general/LICENSE.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/BaseComposition.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/BaseComposition.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/BaseComposition.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/BaseComposition.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/BaseCount.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/BaseCount.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/BaseCount.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/BaseCount.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/COPYING: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/COPYING -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/FastQFile.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/FastQFile.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/FastQFile.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/FastQFile.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/FastQStatus.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/FastQStatus.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/FastQStatus.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/FastQStatus.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/Makefile.depends: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/Makefile.depends -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/test/.gitignore: -------------------------------------------------------------------------------- 1 | fastqTest 2 | results/ 3 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/test/FastQFileTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/test/FastQFileTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/test/FastQValidatorTest.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/test/FastQValidatorTest.sh -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/test/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/test/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/test/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/test/README.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/test/expectedResults/ExpectedResultsFastqTestResults.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/test/expectedResults/ExpectedResultsFastqTestResults.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/fastq/test/testFile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/fastq/test/testFile.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/BaseAsciiMap.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/BaseAsciiMap.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/BaseAsciiMap.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/BaseAsciiMap.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/BaseQualityHelper.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/BaseQualityHelper.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/BaseQualityHelper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/BaseQualityHelper.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/BaseUtilities.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/BaseUtilities.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/BaseUtilities.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/BaseUtilities.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/BasicHash.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/BasicHash.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/BasicHash.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/BasicHash.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/BgzfFileType.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/BgzfFileType.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/BgzfFileType.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/BgzfFileType.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/BgzfFileTypeRecovery.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/BgzfFileTypeRecovery.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/BgzfFileTypeRecovery.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/BgzfFileTypeRecovery.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/CSG_MD5.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/CSG_MD5.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/CharBuffer.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/CharBuffer.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/CharBuffer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/CharBuffer.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Chromosome.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Chromosome.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Chromosome.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Chromosome.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Cigar.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Cigar.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Cigar.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Cigar.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/CigarRoller.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/CigarRoller.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/CigarRoller.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/CigarRoller.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Constant.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Constant.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Error.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Error.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Error.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Error.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/ErrorHandler.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/ErrorHandler.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/ErrorHandler.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/ErrorHandler.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/FileType.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/FileType.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/FileType.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/FileType.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/FortranFormat.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/FortranFormat.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/FortranFormat.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/FortranFormat.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Generic.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Generic.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Generic.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Generic.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/GenomeSequence.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/GenomeSequence.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/GenomeSequence.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/GenomeSequence.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/GenomeSequenceHelpers.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/GenomeSequenceHelpers.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/GenotypeLists.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/GenotypeLists.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/GenotypeLists.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/GenotypeLists.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/GreedyTupleAligner.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/GreedyTupleAligner.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/GzipFileType.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/GzipFileType.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/GzipFileType.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/GzipFileType.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/GzipHeader.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/GzipHeader.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/GzipHeader.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/GzipHeader.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Hash.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Hash.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Hash.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Hash.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/IndexBase.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/IndexBase.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/IndexBase.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/IndexBase.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/InplaceMerge.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/InplaceMerge.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/InplaceMerge.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/InplaceMerge.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Input.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Input.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Input.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Input.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/InputFile.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/InputFile.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/InputFile.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/InputFile.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/IntArray.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/IntArray.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/IntArray.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/IntArray.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/IntHash.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/IntHash.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/IntHash.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/IntHash.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/LICENSE.twister: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/LICENSE.twister -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/LICENSE.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/LongHash.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/LongHash.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/LongInt.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/LongInt.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/LongLongCounter.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/LongLongCounter.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/LongLongCounter.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/LongLongCounter.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Makefile.depends: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Makefile.depends -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MapFunction.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MapFunction.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MapFunction.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MapFunction.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MathConstant.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MathConstant.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MathMatrix.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MathMatrix.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MathMatrix.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MathMatrix.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MathVector.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MathVector.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MathVector.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MathVector.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MemoryAllocators.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MemoryAllocators.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MemoryAllocators.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MemoryAllocators.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MemoryInfo.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MemoryInfo.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MemoryInfo.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MemoryInfo.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MemoryMap.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MemoryMap.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MemoryMap.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MemoryMap.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MemoryMapArray.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MemoryMapArray.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MemoryMapArray.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MemoryMapArray.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MiniDeflate.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MiniDeflate.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/MiniDeflate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/MiniDeflate.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/NonOverlapRegions.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/NonOverlapRegions.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/NonOverlapRegions.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/NonOverlapRegions.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PackedVector.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PackedVector.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Parameters.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Parameters.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Parameters.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Parameters.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Pedigree.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Pedigree.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Pedigree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Pedigree.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreeAlleleFreq.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreeAlleleFreq.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreeAlleleFreq.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreeAlleleFreq.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreeAlleles.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreeAlleles.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreeDescription.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreeDescription.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreeDescription.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreeDescription.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreeFamily.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreeFamily.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreeFamily.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreeFamily.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreeGlobals.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreeGlobals.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreeGlobals.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreeGlobals.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreeLoader.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreeLoader.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreePerson.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreePerson.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreePerson.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreePerson.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreeTrim.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreeTrim.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PedigreeTwin.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PedigreeTwin.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Performance.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Performance.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PhoneHome.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PhoneHome.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/PhoneHome.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/PhoneHome.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/QuickIndex.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/QuickIndex.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/QuickIndex.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/QuickIndex.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Random.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Random.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Random.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Random.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/ReferenceSequence.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/ReferenceSequence.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/ReferenceSequence.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/ReferenceSequence.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/ReusableVector.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/ReusableVector.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/STLUtilities.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/STLUtilities.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/STLUtilities.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/STLUtilities.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/SimpleStats.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/SimpleStats.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/SmithWaterman.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/SmithWaterman.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/SmithWaterman.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/SmithWaterman.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Sort.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Sort.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Sort.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Sort.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/StatGenStatus.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/StatGenStatus.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/StatGenStatus.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/StatGenStatus.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/String.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/String.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/StringAlias.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/StringAlias.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/StringAlias.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/StringAlias.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/StringArray.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/StringArray.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/StringArray.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/StringArray.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/StringBasics.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/StringBasics.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/StringBasics.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/StringBasics.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/StringHash.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/StringHash.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/StringHash.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/StringHash.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/StringMap.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/StringMap.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/StringMap.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/StringMap.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Tabix.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Tabix.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/Tabix.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/Tabix.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/TrimSequence.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/TrimSequence.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/UncompressedFileType.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/UncompressedFileType.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/UncompressedFileType.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/UncompressedFileType.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/UnitTest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/UnitTest.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/glfHandler.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/glfHandler.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/glfHandler.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/glfHandler.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/Chromosome_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/Chromosome_test.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/GenomeSequence_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/GenomeSequence_test.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/GreedyTupleAligner_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/GreedyTupleAligner_test.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/STLUtilities_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/STLUtilities_test.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/TrimSequence_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/TrimSequence_test.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/baseUtilitiesTest/.gitignore: -------------------------------------------------------------------------------- 1 | baseUtilitiesTest 2 | 3 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/baseUtilitiesTest/BaseUtilitiesTest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/baseUtilitiesTest/BaseUtilitiesTest.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/baseUtilitiesTest/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/baseUtilitiesTest/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/cigar/.gitignore: -------------------------------------------------------------------------------- 1 | cigarRollerTest 2 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/cigar/CigarRollerTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/cigar/CigarRollerTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/cigar/CigarRollerTest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/cigar/CigarRollerTest.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/cigar/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/cigar/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/dbsnp/.gitignore: -------------------------------------------------------------------------------- 1 | dbsnpTest 2 | results/ 3 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/dbsnp/Main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/dbsnp/Main.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/dbsnp/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/dbsnp/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/dbsnp/expected/results.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/dbsnp/expected/results.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/dbsnp/testFiles/chr1_partial-bs.umfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/dbsnp/testFiles/chr1_partial-bs.umfa -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/dbsnp/testFiles/chr1_partial.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/dbsnp/testFiles/chr1_partial.fa -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/dbsnp/testFiles/dbsnp.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/dbsnp/testFiles/dbsnp.vcf -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/dbsnp/testFiles/dbsnp.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/dbsnp/testFiles/dbsnp.vcf.gz -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/gtest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/gtest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/.gitignore: -------------------------------------------------------------------------------- 1 | inputFileTest 2 | results/ 3 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/InputFileTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/InputFileTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/InputFileTest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/InputFileTest.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTest.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTest.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTest.glf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTest.glf -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTest.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTest.gz -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTest.txt: -------------------------------------------------------------------------------- 1 | ABCDabcd1234 2 | EFGefg567 3 | hijklHIJKL8910 -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTest2.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTest2.gz -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTest2.txt: -------------------------------------------------------------------------------- 1 | ABCDEFG abcdefg 2 | 123456 hijklm 3 | 1 4 | NOP QRST UVW 5 | 6 | XYZ 789 7 | @#$ -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTestLarge.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTestLarge.bam -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTestLarge.glf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTestLarge.glf -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTestLarge.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTestLarge.gz -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTestLarge.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/data/InputFileTestLarge.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/data/textFile.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/data/textFile.gz -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/data/textFile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/data/textFile.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/expected/results.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/expected/results.log -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/inputFileTest/expected/resultsNoZlib.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/inputFileTest/expected/resultsNoZlib.log -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/memoryMapArrayTest/.gitignore: -------------------------------------------------------------------------------- 1 | memoryMapArrayTest 2 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/memoryMapArrayTest/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/memoryMapArrayTest/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/memoryMapArrayTest/MemoryMapArrayTest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/memoryMapArrayTest/MemoryMapArrayTest.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/nonOverlapRegions/.gitignore: -------------------------------------------------------------------------------- 1 | nonOverlapRegionsTest 2 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/nonOverlapRegions/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/nonOverlapRegions/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/nonOverlapRegions/NonOverlapRegionsTest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/nonOverlapRegions/NonOverlapRegionsTest.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/nonOverlapRegions/expectedNonOverlapRegionsTest.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/nonOverlapRegions/expectedNonOverlapRegionsTest.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/nonOverlapRegions/results/.gitignore: -------------------------------------------------------------------------------- 1 | *.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/packedVectorTest/.gitignore: -------------------------------------------------------------------------------- 1 | packedVectorTest 2 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/packedVectorTest/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/packedVectorTest/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/packedVectorTest/PackedVectorTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/packedVectorTest/PackedVectorTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/packedVectorTest/PackedVectorTest.h: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/phiX.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/phiX.fa -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/referenceSequenceTest/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/referenceSequenceTest/.gitignore -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/referenceSequenceTest/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/referenceSequenceTest/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/referenceSequenceTest/ReferenceSequenceTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/referenceSequenceTest/ReferenceSequenceTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/referenceSequenceTest/ReferenceSequenceTest.h: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/reusableVector/.gitignore: -------------------------------------------------------------------------------- 1 | reusableVectorTest 2 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/reusableVector/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/reusableVector/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/reusableVector/ReusableVectorTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/reusableVector/ReusableVectorTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/reusableVector/ReusableVectorTest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/reusableVector/ReusableVectorTest.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/string/.gitignore: -------------------------------------------------------------------------------- 1 | stringTest 2 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/string/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/string/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/string/StringTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/string/StringTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/string/StringTest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/string/StringTest.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/string/testFiles/testFile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/string/testFiles/testFile.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/test_memmap_data.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/test_memmap_data.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/trimSequence/.gitignore: -------------------------------------------------------------------------------- 1 | trimSequence -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/trimSequence/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/trimSequence/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/general/test/trimSequence/TrimSequence.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/general/test/trimSequence/TrimSequence.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/COPYING: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/COPYING -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/GlfException.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/GlfException.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/GlfException.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/GlfException.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/GlfFile.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/GlfFile.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/GlfFile.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/GlfFile.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/GlfHeader.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/GlfHeader.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/GlfHeader.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/GlfHeader.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/GlfRecord.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/GlfRecord.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/GlfRecord.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/GlfRecord.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/GlfRefSection.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/GlfRefSection.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/GlfRefSection.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/GlfRefSection.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/GlfStatus.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/GlfStatus.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/GlfStatus.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/GlfStatus.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/Makefile.depends: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/Makefile.depends -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/test/.gitignore: -------------------------------------------------------------------------------- 1 | glfTest -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/test/Main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/test/Main.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/test/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/test/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/test/ReadFiles.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/test/ReadFiles.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/test/ReadFiles.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/test/ReadFiles.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/test/Validate.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/test/Validate.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/test/Validate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/test/Validate.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/test/WriteFiles.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/test/WriteFiles.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/test/WriteFiles.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/test/WriteFiles.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/test/results/.gitignore: -------------------------------------------------------------------------------- 1 | MyTestOut* -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/glf/test/testFiles/testGlf.glf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/glf/test/testFiles/testGlf.glf -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/include/.gitignore: -------------------------------------------------------------------------------- 1 | *.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/samtools/COPYING: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/samtools/COPYING -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/samtools/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/samtools/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/samtools/Makefile.depends: -------------------------------------------------------------------------------- 1 | # DO NOT DELETE 2 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/samtools/README.txt: -------------------------------------------------------------------------------- 1 | These files are based on samtools version 981. (retrieved 7/26/11) 2 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/samtools/bam.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/samtools/bam.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/samtools/bgzf.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/samtools/bgzf.c -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/samtools/bgzf.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/samtools/bgzf.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/samtools/khash.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/samtools/khash.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/samtools/knetfile.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/samtools/knetfile.c -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/samtools/knetfile.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/samtools/knetfile.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfFile.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfFile.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfFile.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfFile.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfFileReader.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfFileReader.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfFileReader.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfFileReader.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfFileWriter.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfFileWriter.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfFileWriter.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfFileWriter.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfGenotypeField.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfGenotypeField.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfGenotypeField.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfGenotypeField.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfGenotypeFormat.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfGenotypeFormat.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfGenotypeFormat.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfGenotypeFormat.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfGenotypeSample.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfGenotypeSample.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfGenotypeSample.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfGenotypeSample.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfHeader.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfHeader.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfHeader.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfHeader.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfHelper.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfHelper.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfHelper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfHelper.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfRecord.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfRecord.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfRecord.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfRecord.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfRecordDiscardRules.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfRecordDiscardRules.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfRecordDiscardRules.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfRecordDiscardRules.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfRecordField.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfRecordField.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfRecordField.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfRecordField.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfRecordFilter.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfRecordFilter.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfRecordFilter.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfRecordFilter.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfRecordGenotype.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfRecordGenotype.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfRecordGenotype.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfRecordGenotype.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfRecordInfo.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfRecordInfo.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfRecordInfo.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfRecordInfo.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfSubsetSamples.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfSubsetSamples.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/VcfSubsetSamples.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/VcfSubsetSamples.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/.gitignore: -------------------------------------------------------------------------------- 1 | vcfTest 2 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/Main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/Main.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/Makefile -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/VcfFileTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/VcfFileTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/VcfFileTest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/VcfFileTest.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/VcfHeaderTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/VcfHeaderTest.cpp -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/VcfHeaderTest.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/VcfHeaderTest.h -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/expected/vcfFileNoInfo.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/expected/vcfFileNoInfo.vcf -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/expected/vcfFileNoInfoBGZF.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/expected/vcfFileNoInfoBGZF.vcf -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/expected/vcfFileNoInfoKeepGQHQ.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/expected/vcfFileNoInfoKeepGQHQ.vcf -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/expected/vcfFileNoInfoKeepGT.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/expected/vcfFileNoInfoKeepGT.vcf -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/expected/vcfHeader.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/expected/vcfHeader.vcf -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/results/.gitignore: -------------------------------------------------------------------------------- 1 | *vcf 2 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/testFiles/exclude2.txt: -------------------------------------------------------------------------------- 1 | NA00002 2 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/testFiles/excludeIDs.txt: -------------------------------------------------------------------------------- 1 | rs6054257 2 | microsat1 -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/testFiles/includeIDs.txt: -------------------------------------------------------------------------------- 1 | rs6040355 2 | . 3 | -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/testFiles/subset1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/testFiles/subset1.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/testFiles/subset2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/testFiles/subset2.txt -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/testFiles/testTabix.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/testFiles/testTabix.vcf -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/testFiles/testTabix.vcf.bgzf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/testFiles/testTabix.vcf.bgzf -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/testFiles/testTabix.vcf.bgzf.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/testFiles/testTabix.vcf.bgzf.tbi -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/testFiles/testTabixBadIndex.vcf.bgzf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/testFiles/testTabixBadIndex.vcf.bgzf -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/testFiles/testTabixBadIndex.vcf.bgzf.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/testFiles/testTabixBadIndex.vcf.bgzf.tbi -------------------------------------------------------------------------------- /Library/libStatGenForMinimac3/vcf/test/testFiles/vcfFile.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Library/libStatGenForMinimac3/vcf/test/testFiles/vcfFile.vcf -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Makefile -------------------------------------------------------------------------------- /Makefile.inc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/Makefile.inc -------------------------------------------------------------------------------- /README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/README.txt -------------------------------------------------------------------------------- /copyrights/COPYING: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/copyrights/COPYING -------------------------------------------------------------------------------- /copyrights/LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/copyrights/LICENSE.txt -------------------------------------------------------------------------------- /src/HaplotypeSet.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/HaplotypeSet.cpp -------------------------------------------------------------------------------- /src/HaplotypeSet.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/HaplotypeSet.h -------------------------------------------------------------------------------- /src/Imputation.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/Imputation.cpp -------------------------------------------------------------------------------- /src/Imputation.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/Imputation.h -------------------------------------------------------------------------------- /src/ImputationStatistics.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/ImputationStatistics.cpp -------------------------------------------------------------------------------- /src/ImputationStatistics.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/ImputationStatistics.h -------------------------------------------------------------------------------- /src/Main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/Main.cpp -------------------------------------------------------------------------------- /src/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/Makefile -------------------------------------------------------------------------------- /src/MarkovModel.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/MarkovModel.cpp -------------------------------------------------------------------------------- /src/MarkovModel.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/MarkovModel.h -------------------------------------------------------------------------------- /src/MarkovParameters.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/MarkovParameters.cpp -------------------------------------------------------------------------------- /src/MarkovParameters.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/MarkovParameters.h -------------------------------------------------------------------------------- /src/Unique.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/Unique.cpp -------------------------------------------------------------------------------- /src/Unique.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/src/Unique.h -------------------------------------------------------------------------------- /test/refPanel.m3vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/test/refPanel.m3vcf.gz -------------------------------------------------------------------------------- /test/refPanel.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/test/refPanel.vcf -------------------------------------------------------------------------------- /test/refPanel.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/test/refPanel.vcf.gz -------------------------------------------------------------------------------- /test/refPanelChrX.Non.Auto.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/test/refPanelChrX.Non.Auto.vcf -------------------------------------------------------------------------------- /test/sample.txt.filepart: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/test/sample.txt.filepart -------------------------------------------------------------------------------- /test/targetStudy.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/test/targetStudy.vcf -------------------------------------------------------------------------------- /test/targetStudyChrX.females.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/test/targetStudyChrX.females.vcf -------------------------------------------------------------------------------- /test/targetStudyChrX.males.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Santy-8128/Minimac3/HEAD/test/targetStudyChrX.males.vcf --------------------------------------------------------------------------------