├── .gitignore ├── LICENSE.txt ├── README ├── SimSeqNBProject ├── build.xml ├── build │ ├── built-jar.properties │ ├── classes │ │ └── simseq │ │ │ ├── AddDiploid.class │ │ │ ├── AddError.class │ │ │ ├── FastaReader.class │ │ │ ├── FastaRecord.class │ │ │ ├── Main.class │ │ │ ├── QualityUtil.class │ │ │ ├── SamRecord.class │ │ │ ├── SamWriter.class │ │ │ ├── SeqSampler.class │ │ │ ├── StringBuilderDNA.class │ │ │ └── StringUtil.class │ └── depcache │ │ └── dependencies.txt ├── dist │ ├── README.TXT │ ├── SimSeqNBProject.jar │ └── lib │ │ └── commons-cli-1.2.jar ├── lib │ ├── CopyLibs │ │ └── org-netbeans-modules-java-j2seproject-copylibstask.jar │ ├── bytecode.jar │ ├── commons-cli-1.2-javadoc.jar │ ├── commons-cli-1.2-sources.jar │ ├── commons-cli-1.2.jar │ ├── junit │ │ ├── junit-3.8.2-api.zip │ │ └── junit-3.8.2.jar │ ├── junit_4 │ │ ├── junit-4.5-api.zip │ │ ├── junit-4.5-src.jar │ │ └── junit-4.5.jar │ └── nblibraries.properties ├── manifest.mf ├── nbproject │ ├── build-impl.xml │ ├── configs │ │ ├── addDiploid.properties │ │ └── addError.properties │ ├── genfiles.properties │ ├── private │ │ ├── config.properties │ │ ├── configs │ │ │ ├── addDiploid.properties │ │ │ └── addError.properties │ │ ├── private.properties │ │ ├── private.xml │ │ └── profiler │ │ │ └── configurations.xml │ ├── project.properties │ └── project.xml ├── src │ └── simseq │ │ ├── AddDiploid.java │ │ ├── AddError.java │ │ ├── FastaReader.java │ │ ├── FastaRecord.java │ │ ├── Main.java │ │ ├── QualityUtil.java │ │ ├── SamRecord.java │ │ ├── SamWriter.java │ │ ├── SeqSampler.java │ │ ├── StringBuilderDNA.java │ │ └── StringUtil.java └── store │ └── SimSeq.jar ├── ThirdParty ├── kent │ ├── README │ ├── inc │ │ ├── bPlusTree.h │ │ ├── base64.h │ │ ├── bits.h │ │ ├── cheapcgi.h │ │ ├── common.h │ │ ├── dlist.h │ │ ├── dnaLoad.h │ │ ├── dnaseq.h │ │ ├── dnautil.h │ │ ├── dystring.h │ │ ├── errabort.h │ │ ├── fa.h │ │ ├── filePath.h │ │ ├── hash.h │ │ ├── htmshell.h │ │ ├── https.h │ │ ├── internet.h │ │ ├── kxTok.h │ │ ├── linefile.h │ │ ├── localmem.h │ │ ├── memalloc.h │ │ ├── mime.h │ │ ├── net.h │ │ ├── nib.h │ │ ├── obscure.h │ │ ├── options.h │ │ ├── pipeline.h │ │ ├── portable.h │ │ ├── portimpl.h │ │ ├── sig.h │ │ ├── sqlNum.h │ │ ├── twoBit.h │ │ ├── udc.h │ │ └── verbose.h │ └── lib │ │ ├── bPlusTree.c │ │ ├── base64.c │ │ ├── bits.c │ │ ├── cheapcgi.c │ │ ├── common.c │ │ ├── dlist.c │ │ ├── dnaLoad.c │ │ ├── dnaseq.c │ │ ├── dnautil.c │ │ ├── dystring.c │ │ ├── errabort.c │ │ ├── fa.c │ │ ├── filePath.c │ │ ├── hash.c │ │ ├── htmshell.c │ │ ├── https.c │ │ ├── intExp.c │ │ ├── internet.c │ │ ├── kxTok.c │ │ ├── linefile.c │ │ ├── localmem.c │ │ ├── log.c │ │ ├── log.h │ │ ├── memalloc.c │ │ ├── mime.c │ │ ├── net.c │ │ ├── nib.c │ │ ├── obscure.c │ │ ├── options.c │ │ ├── osunix.c │ │ ├── pipeline.c │ │ ├── portimpl.c │ │ ├── servBrcMcw.c │ │ ├── servCrunx.c │ │ ├── servcis.c │ │ ├── servcl.c │ │ ├── servmsII.c │ │ ├── servpws.c │ │ ├── sqlNum.c │ │ ├── twoBit.c │ │ ├── udc.c │ │ ├── verbose.c │ │ └── wildcmp.c └── samtools │ ├── AUTHORS │ ├── COPYING │ ├── ChangeLog │ ├── ChangeLog.old │ ├── INSTALL │ ├── Makefile │ ├── Makefile.mingw │ ├── NEWS │ ├── bam.c │ ├── bam.h │ ├── bam2bcf.c │ ├── bam2bcf.h │ ├── bam2bcf_indel.c │ ├── bam_aux.c │ ├── bam_color.c │ ├── bam_endian.h │ ├── bam_import.c │ ├── bam_index.c │ ├── bam_lpileup.c │ ├── bam_maqcns.c │ ├── bam_maqcns.h │ ├── 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 │ ├── .gitignore │ ├── Makefile │ ├── README │ ├── bcf.c │ ├── bcf.h │ ├── bcf.tex │ ├── bcf2qcall.c │ ├── bcftools.1 │ ├── bcfutils.c │ ├── call1.c │ ├── fet.c │ ├── index.c │ ├── kfunc.c │ ├── ld.c │ ├── main.c │ ├── prob1.c │ ├── prob1.h │ ├── vcf.c │ └── vcfutils.pl │ ├── bgzf.c │ ├── bgzf.h │ ├── bgzip.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 │ ├── glf.c │ ├── glf.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 │ ├── .gitignore │ ├── 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 │ ├── soap2sam.pl │ ├── varfilter.py │ ├── wgsim.c │ ├── wgsim_eval.pl │ └── zoom2sam.pl │ ├── razf.c │ ├── razf.h │ ├── razip.c │ ├── sam.c │ ├── sam.h │ ├── sam_header.c │ ├── sam_header.h │ ├── sam_view.c │ ├── sample.c │ ├── sample.h │ ├── samtools.1 │ └── win32 │ ├── .gitignore │ ├── libcurses.a │ ├── libz.a │ ├── xcurses.h │ ├── zconf.h │ └── zlib.h ├── cUtils ├── 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