├── .gitignore ├── INSTALL ├── LICENSE ├── README ├── doc ├── Makefile ├── artificial_errors.rst ├── conf.py ├── image_maker.rst ├── index.rst ├── install.rst ├── make.bat ├── plotter3.rst └── synthReadGen.rst ├── example ├── Ecoli_first350k.ale.pdf └── Ecoli_first350k.ale.pdf.png ├── makefile ├── src ├── .gitignore ├── ALE.c ├── ALE.h ├── ALE_low_scores.py ├── ALEhelpers.c ├── ALEhelpers.h ├── ALElike.c ├── ALElike.h ├── CmdIn.py ├── GCcompFinder.c ├── ProgressBar.py ├── SAMcleaner.c ├── Smooth.py ├── ale2wiggle.py ├── artificial_errors.py ├── depth_bias_scripts.py ├── geneTree.c ├── geneTree.h ├── illumina2crossbow.pl ├── image_maker.py ├── makefile ├── mixture.py ├── plotter3.py ├── readFileSplitter.c ├── runBowtieOnPair.sh ├── samtools-0.1.19 │ ├── .gitignore │ ├── AUTHORS │ ├── COPYING │ ├── ChangeLog.old │ ├── INSTALL │ ├── Makefile │ ├── Makefile.mingw │ ├── 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 │ ├── bam_tview.h │ ├── bam_tview_curses.c │ ├── bam_tview_html.c │ ├── bamshuf.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 │ ├── bedcov.c │ ├── bedidx.c │ ├── bgzf.c │ ├── bgzf.h │ ├── bgzip.c │ ├── cut_target.c │ ├── errmod.c │ ├── errmod.h │ ├── examples │ │ ├── 00README.txt │ │ ├── Makefile │ │ ├── bam2bed.c │ │ ├── calDepth.c │ │ ├── chk_indel.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 │ │ ├── ace2sam.c │ │ ├── bamcheck.c │ │ ├── blast2sam.pl │ │ ├── bowtie2sam.pl │ │ ├── export2sam.pl │ │ ├── interpolate_sam.pl │ │ ├── maq2sam.c │ │ ├── md5.c │ │ ├── md5.h │ │ ├── md5fa.c │ │ ├── novo2sam.pl │ │ ├── plot-bamcheck │ │ ├── psl2sam.pl │ │ ├── r2plot.lua │ │ ├── sam2vcf.pl │ │ ├── samtools.pl │ │ ├── soap2sam.pl │ │ ├── varfilter.py │ │ ├── vcfutils.lua │ │ ├── wgsim.c │ │ ├── wgsim_eval.pl │ │ └── zoom2sam.pl │ ├── padding.c │ ├── phase.c │ ├── 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 │ │ ├── xcurses.h │ │ ├── zconf.h │ │ └── zlib.h ├── samtools_helper.c ├── samtools_helper.h ├── sse2neon.h ├── ssw.c ├── ssw.h └── synthReadGen.c └── test ├── 1000.fastq ├── PhiX-SNP.ale ├── PhiX-SNP.ale.SNPreport.txt ├── PhiX-sort.ale ├── PhiX-sort.bam ├── PhiX-tiny-+unmapped-single.sam ├── PhiX-tiny-partial-single.sam ├── PhiX-tiny-partial2-single.sam ├── PhiX-tiny-partial3-single.sam ├── PhiX-tiny-partial4-single.sam ├── PhiX-tiny-partial5-single.sam ├── PhiX-tiny-removed-pair.sam ├── PhiX-tiny-removed2-pair.sam ├── PhiX-tiny-stretch0-pair.sam ├── PhiX-tiny-stretch1-pair.sam ├── PhiX-tiny-stretch2-pair.sam ├── PhiX-tiny-stretch3-pair.sam ├── PhiX-tiny-stretch4-pair.sam ├── PhiX-tiny-stretch5-pair.sam ├── PhiX-tiny-stretch6-pair.sam ├── PhiX-tiny-stretch7-pair.sam ├── PhiX-tiny-stretch8-pair.sam ├── PhiX-tiny-unmapped-single.sam ├── PhiX-tiny.ale ├── PhiX-tiny.sam ├── PhiX.ale ├── PhiX.bam ├── PhiX.sam ├── PhiX174-broken.fsa ├── PhiX174.fsa ├── PhiXbroken-tiny-chimer-pair.sam ├── PhiXbroken-tiny-removed-pair.sam ├── PhiXbroken-tiny-removed2-pair.sam ├── 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