├── .travis.yml ├── Adaptors ├── IlluminaAdaptersAll_nodup.fasta └── IlluminaAdaptersAllpXENpQ108_nodup.fasta ├── BEDFilter ├── BEDFilter.cpp ├── BEDFilter.vcxproj ├── Makefile.am ├── stdafx.cpp └── stdafx.h ├── BEDMerge ├── BEDMerge.cpp ├── BedMerge.vcxproj ├── ChromFeatures.cpp ├── ChromFeatures.h ├── Makefile.am ├── stdafx.cpp └── stdafx.h ├── ChangeLog ├── DNAseqSitePotential ├── DNAseqSitePotential.cpp ├── DNAseqSitePotential.vcxproj ├── Makefile.am ├── stdafx.cpp └── stdafx.h ├── Dockerfile ├── Docs ├── BiokangaAlignerApplicationNote.docx ├── BiokangaAssembApplicationNote.docx ├── BiokangaFilterApplicationNote.docx ├── BiokangaNGSQualityCheckApplicationNote.docx ├── BiokangaSNPCultivarMarkerAssociationApplicationNote.docx ├── BiokangaSNPcalling.docx ├── BiokangaScaffolderApplicationNote.docx ├── Biokanga_4_2_0.docx ├── PacBioKanga_4_2_0.docx ├── biokanga.align.txt ├── biokanga.assemb.txt ├── biokanga.blitz.txt ├── biokanga.contigs.txt ├── biokanga.de2sqlite.txt ├── biokanga.eccontigs.txt ├── biokanga.ecreads.txt ├── biokanga.fasta2nxx.txt ├── biokanga.filtchrom.txt ├── biokanga.filter.txt ├── biokanga.gendeseq.txt ├── biokanga.index.txt ├── biokanga.kmarkers.txt ├── biokanga.kmerdist.txt ├── biokanga.locateroi.txt ├── biokanga.maploci.txt ├── biokanga.markerseqs.txt ├── biokanga.mergeoverlaps.txt ├── biokanga.ngsqc.txt ├── biokanga.pbsim.txt ├── biokanga.pescaffold.txt ├── biokanga.prekmarkers.txt ├── biokanga.pseudogenome.txt ├── biokanga.psl2sqlite.txt ├── biokanga.remaploci.txt ├── biokanga.rnade.txt ├── biokanga.scaffold.txt ├── biokanga.simreads.txt ├── biokanga.snpm2sqlite.txt ├── biokanga.snpmarkers.txt ├── biokanga.snps2sqlite.txt ├── biokanga.sql.schema.txt ├── biokanga.ssr.txt ├── biokanga.swservice.txt ├── biokanga.xfasta.txt ├── pacbiokanga.contigs.txt ├── pacbiokanga.eccontigs.txt ├── pacbiokanga.ecreads.txt ├── pacbiokanga.filter.txt ├── pacbiokanga.kmerdist.txt └── pacbiokanga.swservice.txt ├── FastaToPE ├── FastaToPE.cpp ├── FastaToPE.vcxproj ├── Makefile.am ├── stdafx.cpp └── stdafx.h ├── FindShortApproxMatches ├── FindShortApproxMatches.cpp ├── FindShortApproxMatches.vcxproj ├── Makefile.am ├── stdafx.cpp └── stdafx.h ├── GFFfilter ├── GFFfilter.cpp ├── GFFfilter.vcxproj ├── Makefile.am ├── stdafx.cpp └── stdafx.h ├── GTFfilter ├── ChromMap.cpp ├── ChromMap.h ├── GTFfilter.cpp ├── GTFfilter.vcxproj ├── Makefile.am ├── stdafx.cpp └── stdafx.h ├── HammingDist ├── HammingDist.cpp ├── HammingDist.vcxproj ├── Makefile.am ├── stdafx.cpp └── stdafx.h ├── KangaRADSeq ├── KangaRADSeq.cpp ├── KangaRADSeq.vcxproj ├── ProcReads.cpp ├── StackSeqs.cpp ├── StackSeqs.h ├── stdafx.cpp └── stdafx.h ├── LICENSE ├── LocateROI ├── LocateROI.cpp ├── LocateROI.vcxproj ├── Makefile.am ├── stdafx.cpp └── stdafx.h ├── Loci2Phylip ├── Loci2Phylip.cpp ├── Loci2Phylip.vcxproj ├── Makefile.am ├── stdafx.cpp └── stdafx.h ├── Makefile.am ├── NEWS ├── PEscaffold ├── Makefile.am ├── PEscaffold.cpp ├── PEscaffold.vcxproj ├── SQLiteSummaries.cpp ├── SQLiteSummaries.h ├── stdafx.cpp └── stdafx.h ├── README.md ├── RNAFragSim ├── Makefile.am ├── RNAFragSim.cpp ├── RNAFragSim.h ├── RNAFragSim.vcxproj ├── Transcriptome.cpp ├── Transcriptome.h ├── stdafx.cpp └── stdafx.h ├── RNAseqSitePotential ├── Makefile.am ├── RNAseqSitePotential.cpp ├── RNAseqSitePotential.vcxproj ├── stdafx.cpp └── stdafx.h ├── SSRdiscovery ├── Makefile.am ├── SQLiteSummaries.cpp ├── SQLiteSummaries.h ├── SSRIdentify.cpp ├── SSRIdentify.h ├── SSRdiscovery.cpp ├── SSRdiscovery.vcxproj ├── stdafx.cpp └── stdafx.h ├── Script ├── assemb_GSS_Group1_illumadapts.py └── script_readme.txt ├── SimulateMNase ├── Makefile.am ├── SimulateMNase.cpp ├── SimulateMNase.vcxproj ├── stdafx.cpp └── stdafx.h ├── appveyor.yml ├── bed2csv ├── Makefile.am ├── bed2csv.cpp ├── bed2csv.vcxproj ├── stdafx.cpp └── stdafx.h ├── biokanga.sln ├── biokanga ├── Aligner.cpp ├── Aligner.h ├── AlignsBootstrap.cpp ├── AlignsBootstrap.h ├── ArtefactReduce.cpp ├── ArtefactReduce.h ├── AssembGraph.cpp ├── AssembGraph.h ├── Assemble.cpp ├── Blitz.cpp ├── Blitz.h ├── FastaNxx.cpp ├── FastaNxx.h ├── FilterSAMAlignments.cpp ├── FilterSAMAlignments.h ├── Kangadna.cpp ├── Kangadna.h ├── LocKMers.cpp ├── LocKMers.h ├── LocateROI.cpp ├── LocateROI.h ├── Makefile.am ├── MapLoci2Feat.cpp ├── MapLoci2Feat.h ├── MarkerKMers.cpp ├── MarkerKMers.h ├── MarkerSeq.cpp ├── MarkerSeq.h ├── Markers.cpp ├── Markers.h ├── MergeReadPairs.cpp ├── MergeReadPairs.h ├── PEScaffold.cpp ├── PEScaffold.h ├── ReadStats.cpp ├── ReadStats.h ├── RemapLoci.cpp ├── RemapLoci.h ├── SNPLoci.cpp ├── SNPLoci.h ├── SQLiteDE.cpp ├── SQLiteDE.h ├── SQLiteMarkers.cpp ├── SQLiteMarkers.h ├── SQLitePSL.cpp ├── SQLitePSL.h ├── SQLiteSummaries.cpp ├── SQLiteSummaries.h ├── SSRdiscovery.cpp ├── SSRdiscovery.h ├── Scaffolder.cpp ├── Scaffolder.h ├── SimReads.cpp ├── SimReads.h ├── biokanga.cpp ├── biokanga.h ├── biokanga.vcxproj ├── csv2sqlite.cpp ├── deNovoAssemb.cpp ├── deNovoAssemb.h ├── fastaextract.cpp ├── genDESeq.cpp ├── genkmarkers.cpp ├── genmarkerseq.cpp ├── genpseudogenome.cpp ├── gensnpmarkers.cpp ├── kanga.cpp ├── kanga.h ├── kangade.cpp ├── kangax.cpp ├── kangax.h ├── kmermarkers.cpp ├── makestatic.sh ├── maploci2features.cpp ├── mergeoverlaps.cpp ├── psl2sqlite.cpp ├── stdafx.cpp └── stdafx.h ├── blast2csv ├── Makefile.am ├── blast2csv.cpp ├── blast2csv.vcxproj ├── stdafx.cpp └── stdafx.h ├── configure.ac ├── csv2bed ├── Makefile.am ├── csv2bed.cpp ├── csv2bed.vcxproj ├── stdafx.cpp └── stdafx.h ├── csv2fasta ├── IncExclChroms.cpp ├── IncExclChroms.h ├── Makefile.am ├── csv2fasta.cpp ├── csv2fasta.vcxproj ├── stdafx.cpp └── stdafx.h ├── csv2feat ├── Makefile.am ├── csv2feat.cpp ├── csv2feat.vcxproj ├── stdafx.cpp └── stdafx.h ├── csv2sqlite ├── Makefile.am ├── SQLiteDE.cpp ├── SQLiteDE.h ├── SQLiteMarkers.cpp ├── SQLiteMarkers.h ├── csv2sqlite.cpp ├── csv2sqlite.vcxproj ├── stdafx.cpp └── stdafx.h ├── csv2stats ├── Makefile.am ├── csv2stats.cpp ├── csv2stats.vcxproj ├── stdafx.cpp └── stdafx.h ├── csvfilter ├── CSVFilter.vcxproj ├── Makefile.am ├── csvfilter.cpp ├── stdafx.cpp └── stdafx.h ├── csvmerge ├── CSVMerge.vcxproj ├── ChromMaps.cpp ├── ChromMaps.h ├── Makefile.am ├── csvmerge.cpp ├── stdafx.cpp └── stdafx.h ├── dmpbioseq ├── Makefile.am ├── dmpbioseq.cpp ├── dmpbioseq.vcxproj ├── stdafx.cpp └── stdafx.h ├── fasta2bed ├── Makefile.am ├── fasta2bed.cpp ├── fasta2bed.vcxproj ├── stdafx.cpp └── stdafx.h ├── fasta2dist ├── Makefile.am ├── fasta2dist.cpp ├── fasta2dist.vcxproj ├── stdafx.cpp └── stdafx.h ├── fasta2struct ├── Makefile.am ├── fasta2struct.cpp ├── fasta2struct.vcxproj ├── stdafx.cpp └── stdafx.h ├── fastafilter ├── Makefile.am ├── fastafilter.cpp ├── fastafilter.vcxproj ├── stdafx.cpp └── stdafx.h ├── filterreads ├── Makefile.am ├── filterreads.cpp ├── filterreads.vcxproj ├── stdafx.cpp └── stdafx.h ├── genDESeq ├── Makefile.am ├── genDESeq.cpp ├── genDESeq.vcxproj ├── stdafx.cpp └── stdafx.h ├── genElementProfiles ├── Makefile.am ├── genElementProfiles.cpp ├── genElementProfiles.vcxproj ├── stdafx.cpp └── stdafx.h ├── genGenomeFromAGP ├── AGPs.cpp ├── AGPs.h ├── Contigs.cpp ├── Contigs.h ├── Makefile.am ├── genGenomeFromAGP.cpp ├── genGenomeFromAGP.vcxproj ├── stdafx.cpp └── stdafx.h ├── genNormWiggle ├── Makefile.am ├── genNormWiggle.cpp ├── genNormWiggle.vcxproj ├── stdafx.cpp └── stdafx.h ├── genWiggle ├── Makefile.am ├── genWiggle.cpp ├── genWiggle.vcxproj ├── stdafx.cpp └── stdafx.h ├── genalignconf ├── AlignRecip.cpp ├── AlignRecip.h ├── AlignSubSeqs.cpp ├── AlignSubSeqs.h ├── Makefile.am ├── genalignconf.cpp ├── genalignconf.vcxproj ├── stdafx.cpp └── stdafx.h ├── genalignloci2core ├── Makefile.am ├── genalignloci2core.cpp ├── genalignloci2core.vcxproj ├── stdafx.cpp └── stdafx.h ├── genalignref2relloci ├── FilterRefIDs.cpp ├── FilterRefIDs.h ├── Makefile.am ├── genalignref2relloci.cpp ├── genalignref2relloci.vcxproj ├── stdafx.cpp └── stdafx.h ├── genalignstats ├── Makefile.am ├── genalignstats.cpp ├── genalignstats.vcxproj ├── stdafx.cpp └── stdafx.h ├── genbiobed ├── Makefile.am ├── genbiobed.cpp ├── genbiobed.vcxproj ├── stdafx.cpp └── stdafx.h ├── genbiomultialign ├── Makefile.am ├── genbiomultialign.cpp ├── genbiomultialign.vcxproj ├── stdafx.cpp └── stdafx.h ├── genbioseq ├── Makefile.am ├── genbioseq.cpp ├── genbioseq.vcxproj ├── stdafx.cpp └── stdafx.h ├── gencentroidmetrics ├── Makefile.am ├── SNPsFile.cpp ├── SNPsFile.h ├── gencentroidmetrics.cpp ├── gencentroidmetrics.vcxproj ├── stdafx.cpp └── stdafx.h ├── gencomposition ├── Makefile.am ├── gencomposition.cpp ├── gencomposition.vcxproj ├── gencomposition.vcxproj.user ├── stdafx.cpp └── stdafx.h ├── genelementseq ├── Makefile.am ├── genelementseq.cpp ├── genelementseq.vcxproj ├── stdafx.cpp └── stdafx.h ├── genhyperconserved ├── Makefile.am ├── genhyperconserved.cpp ├── genhyperconserved.vcxproj ├── stdafx.cpp └── stdafx.h ├── genhyperdropouts ├── Makefile.am ├── genhyperdropouts.cpp ├── genhyperdropouts.vcxproj ├── stdafx.cpp └── stdafx.h ├── genloci2gene ├── Makefile.am ├── genloci2gene.cpp ├── genloci2gene.vcxproj ├── stdafx.cpp └── stdafx.h ├── genmarkers ├── Makefile.am ├── Markers.cpp ├── Markers.h ├── genmarkers.cpp ├── genmarkers.h ├── genmarkers.vcxproj ├── stdafx.cpp └── stdafx.h ├── gennucstats ├── IncExclChroms.cpp ├── IncExclChroms.h ├── Makefile.am ├── gennucstats.cpp ├── gennucstats.vcxproj ├── stdafx.cpp └── stdafx.h ├── genpseudogenome ├── Makefile.am ├── genpseudogenome.cpp ├── genpseudogenome.vcxproj ├── stdafx.cpp └── stdafx.h ├── genrollups ├── Makefile.am ├── genrollups.cpp ├── genrollups.vcxproj ├── stdafx.cpp └── stdafx.h ├── gensampler ├── Makefile.am ├── gensampler.cpp ├── gensampler.vcxproj ├── stdafx.cpp └── stdafx.h ├── genseqcandidates ├── IncExclChroms.cpp ├── IncExclChroms.h ├── Makefile.am ├── genseqcandidates.cpp ├── genseqcandidates.vcxproj ├── stdafx.cpp └── stdafx.h ├── genstructprofile ├── Makefile.am ├── genstructprofile.cpp ├── genstructprofile.vcxproj ├── stdafx.cpp └── stdafx.h ├── genstructstats ├── Makefile.am ├── genstructstats.cpp ├── genstructstats.vcxproj ├── stdafx.cpp └── stdafx.h ├── genultras ├── Makefile.am ├── genultras.cpp ├── genultras.vcxproj ├── stdafx.cpp └── stdafx.h ├── genzygosity ├── Makefile.am ├── genzygosity.cpp ├── genzygosity.h ├── genzygosity.vcxproj ├── stdafx.cpp └── stdafx.h ├── hooks └── post_push ├── kangahrdx ├── HomozyReduce.cpp ├── HomozyReduce.h ├── LoadContigs.cpp ├── Makefile.am ├── kangahrdx.cpp ├── kangahrdx.vcxproj ├── stdafx.cpp └── stdafx.h ├── kangapr ├── Makefile.am ├── ProcReads.cpp ├── ProcReads.h ├── SampleReads.cpp ├── SampleReads.h ├── kangapr.cpp ├── kangapr.h ├── kangapr.vcxproj ├── stdafx.cpp └── stdafx.h ├── kangar ├── Makefile.am ├── kangar.cpp ├── kangar.vcxproj ├── stdafx.cpp └── stdafx.h ├── kangarg ├── Makefile.am ├── kangarg.cpp ├── kangarg.vcxproj ├── stdafx.cpp └── stdafx.h ├── libBKPLPlot ├── BKPLPlot.cpp ├── BKPLPlot.h ├── BKPlots.cpp ├── EmbeddedPalettes.h ├── Makefile.am ├── csa.cpp ├── csa.h ├── dirent_msvc.h ├── disptab.h ├── drivers.h ├── dspline.cpp ├── dspline.h ├── dsplint.cpp ├── dsplint.h ├── libBKPLPlot.vcxproj ├── ltdl_win32.cpp ├── ltdl_win32.h ├── mem.cpp ├── metadefs.h ├── mt19937ar.cpp ├── mt19937ar.h ├── nan.h ├── pdf.h ├── pdfutils.cpp ├── plConfig.h ├── plDevs.h ├── plaffine.cpp ├── plarc.cpp ├── plargs.cpp ├── plbox.cpp ├── plbuf.cpp ├── plcont.cpp ├── plcore.cpp ├── plcore.h ├── plctrl.cpp ├── plcvt.cpp ├── pldebug.h ├── pldll.h ├── pldtik.cpp ├── plevent.h ├── plf2ops.cpp ├── plfci-truetype.h ├── plfci-type1.h ├── plfill.cpp ├── plfreetype.cpp ├── plfreetype.h ├── plgradient.cpp ├── plgridd.cpp ├── plhershey-unicode.h ├── plhist.cpp ├── plimage.cpp ├── pllegend.cpp ├── plline.cpp ├── plmap.cpp ├── plot3d.cpp ├── plpage.cpp ├── plplot.h ├── plplotP.h ├── plplot_config.h ├── plplotcanvas-hacktext.h ├── plplotcanvas.h ├── plsdef.cpp ├── plshade.cpp ├── plstdio.cpp ├── plstnd5.fnt.h ├── plstripc.cpp ├── plstrm.h ├── plsym.cpp ├── pltick.cpp ├── pltime.cpp ├── plunicode-type1.h ├── plvect.cpp ├── plvpor.cpp ├── plwind.cpp ├── plxtnd5.fnt.h ├── plxwd.h ├── ps.h ├── qsastime.cpp ├── qsastime.h ├── qsastimeP.h ├── qsastime_extra.cpp ├── qsastime_extra.h ├── qsastimedll.h ├── qt.h ├── resource.h ├── stdafx.cpp ├── stdafx.h ├── svg.cpp ├── tai-utc.h └── targetver.h ├── libbiokanga ├── AlignValidate.cpp ├── AlignValidate.h ├── BEDfile.cpp ├── BEDfile.h ├── BioSeqFile.cpp ├── BioSeqFile.h ├── CSVFile.cpp ├── CSVFile.h ├── CVS2BED.cpp ├── CVS2BED.h ├── Centroid.cpp ├── Centroid.h ├── ConfSW.cpp ├── ConfSW.h ├── Conformation.cpp ├── Conformation.h ├── Contaminants.cpp ├── Contaminants.h ├── DSsort.cpp ├── DSsort.h ├── DataPoints.cpp ├── DataPoints.h ├── Diagnostics.cpp ├── Diagnostics.h ├── Endian.cpp ├── Endian.h ├── ErrorCodes.cpp ├── ErrorCodes.h ├── FMIndex.cpp ├── FMIndex.h ├── Fasta.cpp ├── Fasta.h ├── FeatLoci.cpp ├── FeatLoci.h ├── FilterLoci.cpp ├── FilterLoci.h ├── FilterRefIDs.cpp ├── FilterRefIDs.h ├── GFFFile.cpp ├── GFFFile.h ├── GOAssocs.cpp ├── GOAssocs.h ├── GOTerms.cpp ├── GOTerms.h ├── GTFFile.cpp ├── GTFFile.h ├── HashFile.cpp ├── HashFile.h ├── HyperEls.cpp ├── HyperEls.h ├── MAlignFile.cpp ├── MAlignFile.h ├── MTqsort.cpp ├── MTqsort.h ├── Makefile.am ├── MemAlloc.cpp ├── MemAlloc.h ├── NeedlemanWunsch.cpp ├── NeedlemanWunsch.h ├── ProcRawReads.cpp ├── ProcRawReads.h ├── Random.cpp ├── Random.h ├── RsltsFile.cpp ├── RsltsFile.h ├── SAMfile.cpp ├── SAMfile.h ├── SeqTrans.cpp ├── SeqTrans.h ├── SfxArray.cpp ├── SfxArray.h ├── SfxArrayV2.cpp ├── SfxArrayV2.h ├── Shuffle.cpp ├── Shuffle.h ├── SimpleGlob.h ├── SimpleRNG.cpp ├── SimpleRNG.h ├── SmithWaterman.cpp ├── SmithWaterman.h ├── Stats.cpp ├── Stats.h ├── StopWatch.cpp ├── StopWatch.h ├── Twister.cpp ├── Twister.h ├── Utility.cpp ├── Utility.h ├── VisData.cpp ├── VisData.h ├── argtable2.cpp ├── argtable2.h ├── bgzf.cpp ├── bgzf.h ├── commdefs.h ├── commhdrs.h ├── conservlib.cpp ├── conservlib.h ├── fmindexpriv.h ├── libbiokanga.vcxproj ├── sais.cpp ├── sais.h ├── sqlite3.c ├── sqlite3.h ├── sqlite3ext.h ├── stdafx.cpp ├── stdafx.h ├── str.h ├── str_impadvanced.cpp ├── str_implement.cpp ├── str_support1.h ├── str_support2.h ├── targetver.h └── zlib │ ├── libz.a │ ├── zconf.h │ └── zlib.h ├── loci2dist ├── Makefile.am ├── loci2dist.cpp ├── loci2dist.vcxproj ├── stdafx.cpp └── stdafx.h ├── locmarkers ├── LocKMers.cpp ├── LocKMers.h ├── Makefile.am ├── locmarkers.cpp ├── locmarkers.vcxproj ├── stdafx.cpp └── stdafx.h ├── maploci2features ├── Makefile.am ├── maploci2features.cpp ├── maploci2features.vcxproj ├── stdafx.cpp └── stdafx.h ├── pacbiokanga ├── AssembGraph.cpp ├── AssembGraph.h ├── BKSProvider.cpp ├── BKSProvider.h ├── BKSRequester.cpp ├── BKSRequester.h ├── BKScommon.h ├── MAConsensus.cpp ├── MAConsensus.h ├── MAFKMerDist.cpp ├── MAFKMerDist.h ├── Makefile.am ├── PBAssemb.cpp ├── PBAssemb.h ├── PBECContigs.cpp ├── PBECContigs.h ├── PBErrCorrect.cpp ├── PBErrCorrect.h ├── PBFilter.cpp ├── PBFilter.h ├── PBSWService.cpp ├── PBSWService.h ├── PacBioUtility.cpp ├── PacBioUtility.h ├── SQLiteSummaries.cpp ├── SQLiteSummaries.h ├── SSW.cpp ├── SSW.h ├── SWAlign.cpp ├── SWAlign.h ├── SeqStore.cpp ├── SeqStore.h ├── makestatic.sh ├── pacbiocommon.h ├── pacbiokanga.cpp ├── pacbiokanga.h ├── pacbiokanga.vcxproj ├── stdafx.cpp └── stdafx.h ├── predconfnucs ├── Makefile.am ├── predconfnucs.cpp ├── predconfnucs.vcxproj ├── stdafx.cpp └── stdafx.h ├── prednucleosomes ├── Makefile.am ├── prednucleosomes.cpp ├── prednucleosomes.vcxproj ├── stdafx.cpp └── stdafx.h ├── proccentroids ├── Makefile.am ├── proccentroids.cpp ├── proccentroids.vcxproj ├── stdafx.cpp └── stdafx.h ├── processcsvfiles ├── Makefile.am ├── ProcessCSVfiles.cpp ├── ProcessCSVfiles.vcxproj ├── stdafx.cpp └── stdafx.h ├── psl2csv ├── Makefile.am ├── psl2csv.cpp ├── psl2csv.vcxproj ├── stdafx.cpp └── stdafx.h ├── quickcount ├── Makefile.am ├── quickcount.cpp ├── quickcount.vcxproj ├── stdafx.cpp └── stdafx.h ├── splitmultifasta ├── Makefile.am ├── splitmultifasta.cpp ├── splitmultifasta.vcxproj ├── stdafx.cpp └── stdafx.h ├── ufilter ├── IncExclChroms.cpp ├── IncExclChroms.h ├── Makefile.am ├── stdafx.cpp ├── stdafx.h ├── ufilter.cpp └── ufilter.vcxproj ├── uhamming ├── Makefile.am ├── cHamming.cpp ├── cHamming.s ├── foo.lst ├── stdafx.cpp ├── stdafx.h ├── uhamming.cpp └── uhamming.vcxproj ├── usimdiffexpr ├── Makefile.am ├── stdafx.cpp ├── stdafx.h ├── usimdiffexpr.cpp └── usimdiffexpr.vcxproj └── zlibstatic ├── adler32.c ├── compress.c ├── crc32.c ├── crc32.h ├── deflate.c ├── deflate.h ├── gzclose.c ├── gzguts.h ├── gzlib.c ├── gzread.c ├── gzwrite.c ├── infback.c ├── inffast.c ├── inffast.h ├── inffixed.h ├── inflate.c ├── inflate.h ├── inftrees.c ├── inftrees.h ├── stdafx.cpp ├── stdafx.h ├── targetver.h ├── trees.c ├── trees.h ├── uncompr.c ├── zconf.h ├── zlib.h ├── zlibstatic.vcxproj ├── zutil.c └── zutil.h /.travis.yml: 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