├── .gitignore ├── .travis.yml ├── AnnotationInputFile.h ├── AnnotationOutput.h ├── AnnotationOutputFile.h ├── AnnotationResult.h ├── AnnotationResultCollection.h ├── AnnotationString.h ├── Argument.h ├── BedReader.h ├── COPYING ├── Codon.h ├── Common.h ├── FreqTable.h ├── Gene.h ├── GeneAnnotation.h ├── GeneFormat.h ├── GenomeScore.h ├── GenomeSequence.h ├── GitVersion.h ├── IO.cpp ├── IO.h ├── LICENSE ├── LineBreaker.h ├── LogFile.cpp ├── LogFile.h ├── Main.cpp ├── Makefile ├── ModelParser.h ├── OrderedMap.h ├── Priority.h ├── README ├── README.md ├── README.wiki ├── Range.h ├── SequenceUtil.h ├── StringTemplate.h ├── StringUtil.h ├── TODO ├── TabixReader.h ├── Type.h ├── TypeConversion.h ├── codon.txt ├── createGenomeScore.cpp ├── example ├── correct.100.refGene.vcf ├── correct.100.refGene.vcf.anno.frq ├── correct.100.refGene.vcf.base.frq ├── correct.100.refGene.vcf.codon.frq ├── correct.100.refGene.vcf.gz ├── correct.100.refGene.vcf.gz.tbi ├── correct.100.refGene.vcf.indel.frq ├── correct.100.refGene.vcf.log ├── correct.100.refGene.vcf.top.anno.frq ├── correct.100.vcf ├── correct.100.vcf.anno.frq ├── correct.100.vcf.base.frq ├── correct.100.vcf.codon.frq ├── correct.100.vcf.indel.frq ├── correct.100.vcf.log ├── correct.100.vcf.top.anno.frq ├── correct.epacts ├── correct.epacts.anno.frq ├── correct.epacts.base.frq ├── correct.epacts.codon.frq ├── correct.epacts.indel.frq ├── correct.epacts.log ├── correct.epacts.top.anno.frq ├── correct.noref.100.vcf ├── correct.noref.100.vcf.anno.frq ├── correct.noref.100.vcf.base.frq ├── correct.noref.100.vcf.codon.frq ├── correct.noref.100.vcf.indel.frq ├── correct.noref.100.vcf.log ├── correct.noref.100.vcf.top.anno.frq ├── correct.test.plain.txt ├── correct.test.plain.txt.anno.frq ├── correct.test.plain.txt.base.frq ├── correct.test.plain.txt.codon.frq ├── correct.test.plain.txt.indel.frq ├── correct.test.plain.txt.log ├── correct.test.plain.txt.top.anno.frq ├── correct.test.vcf ├── correct.test.vcf.anno.frq ├── correct.test.vcf.base.frq ├── correct.test.vcf.codon.frq ├── correct.test.vcf.indel.frq ├── correct.test.vcf.log ├── correct.test.vcf.top.anno.frq ├── correct.test2.plain.txt.gz ├── correct.test2.plain.txt.gz.tbi ├── correct.test3.plain.txt.gz ├── correct.test3.plain.txt.gz.tbi ├── correct.testBedReader ├── correct.testGenomeScore ├── correct.testTabixReader ├── input.100.vcf.gz ├── input.epacts ├── input.test.epacts ├── input.test.plain.txt ├── input.test.vcf ├── input.test2.plain.txt ├── input.test3.plain.txt ├── test.fa ├── test.fa.fai └── test.gene.txt ├── ext └── wiki2html.jar ├── priority.epact.txt ├── priority.txt ├── resources └── download.sh ├── testBedReader.cpp ├── testGenomeScore.cpp ├── testLineBreaker.cpp ├── testStringTemplate.cpp ├── testTabixReader.cpp └── third ├── .gitignore ├── Makefile └── tabix-0.2.6.tar.bz2 /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zhanxw/anno/HEAD/.gitignore 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