├── .gitignore ├── 2bwt-flex ├── 2BWT-Builder.c ├── HOCC.c ├── HOCC.h ├── HOCCConstruct.c ├── HOCCConstruct.h ├── LT.c ├── LT.h ├── LTConstruct.c ├── LTConstruct.h ├── Makefile ├── OCC.h ├── Release.h ├── SRA2BWTCheckAndExtend.c ├── SRA2BWTCheckAndExtend.h ├── SRA2BWTMdl.c ├── SRA2BWTMdl.h ├── SRAArguments.h ├── SRACore.c ├── SRACore.h └── pair-end │ ├── Makefile │ ├── PEAlgnmt.c │ ├── PEAlgnmt.h │ ├── make.sh │ ├── pair-end-release.txt │ ├── pair-end-v1.0.0-readme.txt │ └── testDrive.c ├── 2bwt-lib ├── 2BWT-Builder.c ├── 2BWT-Interface.c ├── 2BWT-Interface.h ├── 2BWT-Sample.c ├── 2bwt-builder.ini ├── 2bwt-readme.templt ├── 2bwt-readme.txt ├── BWT.c ├── BWT.h ├── BWTConstruct.c ├── BWTConstruct.h ├── BWTLoad.c ├── BWTLoad.h ├── BlastCompare.c ├── CacheTest.c ├── DNACount.c ├── DNACount.h ├── FASTAToText.c ├── HSP.c ├── HSP.h ├── HSPstatistic.c ├── HSPstatistic.h ├── IndexCtl.c ├── IndexCtl.h ├── Makefile ├── MemManager.c ├── MemManager.h ├── MiscUtilities.c ├── MiscUtilities.h ├── QSufSort.c ├── QSufSort.h ├── Release.h ├── SSETest.c ├── SearchBWT.c ├── Socket.c ├── Socket.h ├── TextConverter.c ├── TextConverter.h ├── Timing.c ├── Timing.h ├── TypeNLimit.h ├── blast_dust.c ├── blast_dust.h ├── devTools │ ├── 2BWT-Benchmark.c │ └── Makefile ├── dictionary.c ├── dictionary.h ├── iniparser.c ├── iniparser.h ├── inistrlib.c ├── inistrlib.h ├── karlin.c ├── karlin.h ├── mm_malloc.h ├── r250.c └── r250.h ├── AlgnResult.cpp ├── AlgnResult.h ├── BGS-Build.cpp ├── BGS-Experiment.log ├── BGS-HostAlgnmtAlgo2.cpp ├── BGS-HostAlgnmtAlgo2.h ├── BGS-HostAlgnmtAlgoSingle.cpp ├── BGS-HostAlgnmtAlgoSingle.h ├── BGS-IO.cpp ├── BGS-IO.h ├── BGS-ReleaseGuide.log ├── BGS-TestNote.log ├── BGS-View-PE.cpp ├── BGS-View.cpp ├── CPUfunctions.cpp ├── CPUfunctions.h ├── DV-DPForBothUnalign.cu ├── DV-DPForBothUnalign.h ├── DV-DPForSingleReads.cu ├── DV-DPForSingleReads.h ├── DV-DPfunctions.cu ├── DV-DPfunctions.h ├── DV-Kernel.cu ├── DV-Kernel.h ├── DV-SemiDP.cu ├── DV-SemiDP.h ├── FileUtilities.cpp ├── FileUtilities.h ├── HSPAux.h ├── IndexHandler.cpp ├── IndexHandler.h ├── IniParam.cpp ├── IniParam.h ├── Makefile ├── OutputDPResult.cpp ├── OutputDPResult.h ├── PE.cpp ├── PE.h ├── PEAlgnmt.cpp ├── PEAlgnmt.h ├── QueryParser.cpp ├── QueryParser.h ├── README.md ├── Release.h ├── SAList.cpp ├── SAList.h ├── SAM.cpp ├── SAM.h ├── SOAP3-DP.cu ├── UsageInterface.cpp ├── UsageInterface.h ├── aio_thread.cpp ├── aio_thread.h ├── alignment.cu ├── alignment.h ├── definitions.h ├── global_arrays.cpp ├── global_arrays.h ├── sample.cu ├── samtools-0.1.18 ├── AUTHORS ├── COPYING ├── ChangeLog ├── INSTALL ├── Makefile.mingw ├── Makefile.original ├── NEWS ├── bam.c ├── bam.h ├── bam2bcf.c ├── bam2bcf.h ├── bam2bcf_indel.c ├── bam2depth.c ├── bam_aux.c ├── bam_cat.c ├── bam_color.c ├── bam_endian.h ├── bam_import.c ├── bam_index.c ├── bam_lpileup.c ├── bam_mate.c ├── bam_md.c ├── bam_pileup.c ├── bam_plcmd.c ├── bam_reheader.c ├── bam_rmdup.c ├── bam_rmdupse.c ├── bam_sort.c ├── bam_stat.c ├── bam_tview.c ├── bamtk.c ├── bcftools │ ├── Makefile │ ├── README │ ├── bcf.c │ ├── bcf.h │ ├── bcf.tex │ ├── bcf2qcall.c │ ├── bcfutils.c │ ├── call1.c │ ├── em.c │ ├── fet.c │ ├── index.c │ ├── kfunc.c │ ├── kmin.c │ ├── kmin.h │ ├── main.c │ ├── mut.c │ ├── prob1.c │ ├── prob1.h │ ├── vcf.c │ └── vcfutils.pl ├── bedidx.c ├── bgzf.c ├── bgzf.h ├── bgzip.c ├── cut_target.c ├── errmod.c ├── errmod.h ├── examples │ ├── 00README.txt │ ├── Makefile │ ├── bam2bed.c │ ├── calDepth.c │ ├── ex1.fa │ ├── ex1.sam.gz │ ├── toy.fa │ └── toy.sam ├── faidx.c ├── faidx.h ├── kaln.c ├── kaln.h ├── khash.h ├── klist.h ├── knetfile.c ├── knetfile.h ├── kprobaln.c ├── kprobaln.h ├── kseq.h ├── ksort.h ├── kstring.c ├── kstring.h ├── misc │ ├── HmmGlocal.java │ ├── Makefile │ ├── blast2sam.pl │ ├── bowtie2sam.pl │ ├── export2sam.pl │ ├── interpolate_sam.pl │ ├── maq2sam.c │ ├── md5.c │ ├── md5.h │ ├── md5fa.c │ ├── novo2sam.pl │ ├── psl2sam.pl │ ├── sam2vcf.pl │ ├── samtools.pl │ ├── 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