├── LICENSE ├── Makefile ├── README ├── README.md ├── VERSION ├── bactsnp.sh ├── benchmark ├── NASP_get_config.sh ├── TTR_fasta2snp │ ├── Makefile │ ├── README │ ├── example.fasta_list │ ├── fuga.cc │ ├── fuga.h │ ├── hoge.cc │ ├── hoge.h │ └── main.cc ├── TTR_get_config.sh ├── TTR_get_newick.sh ├── TTR_run_paup.sh ├── get_snp_cfsan │ ├── Makefile │ ├── hoge.cc │ ├── hoge.h │ └── main.cc ├── get_snp_cortex │ ├── Makefile │ ├── hoge.cc │ ├── hoge.h │ └── main.cc ├── get_snp_freebayes │ ├── Makefile │ ├── hoge.cc │ ├── hoge.h │ └── main.cc ├── get_snp_gatk │ ├── Makefile │ ├── main.cc │ ├── two_matrix.cc │ └── two_matrix.h ├── get_snp_nasp │ ├── Makefile │ └── main.cc ├── get_snp_phenix │ ├── Makefile │ ├── fuga.cc │ ├── fuga.h │ ├── hoge.cc │ ├── hoge.h │ └── main.cc ├── get_snp_samtools │ ├── Makefile │ ├── main.cc │ ├── two_matrix.cc │ └── two_matrix.h ├── get_snp_snippy │ ├── Makefile │ └── main.cc ├── get_snp_varscan │ ├── Makefile │ ├── fuga.cc │ ├── fuga.h │ ├── hoge.h │ └── main.cc └── move_snp │ ├── Makefile │ ├── fuga.cc │ ├── fuga.h │ ├── hoge.cc │ ├── hoge.h │ └── main.cc ├── others ├── fa_list_format ├── fq_list_format ├── input_region_format ├── picard │ ├── LICENSE.txt │ ├── a │ └── picard.jar └── platanus_warning ├── src ├── Platanus │ ├── ChangeLog │ ├── LICENSE │ ├── Makefile │ ├── README │ ├── assemble.cpp │ ├── assemble.h │ ├── baseCommand.cpp │ ├── baseCommand.h │ ├── binstr.h │ ├── common.cpp │ ├── common.h │ ├── counter.h │ ├── doubleHash.h │ ├── gapClose.cpp │ ├── gapClose.h │ ├── gapCloseDBG.h │ ├── gapCloseOLC.cpp │ ├── gapCloseOLC.h │ ├── graph.h │ ├── kmer.h │ ├── main.cpp │ ├── mapper.cpp │ ├── mapper.h │ ├── scaffold.cpp │ ├── scaffold.h │ ├── scaffoldGraph.cpp │ ├── scaffoldGraph.h │ ├── seqlib.cpp │ └── seqlib.h ├── Platanus_trim │ ├── LICENSE │ ├── Makefile │ ├── README_Jap.txt │ ├── binstr.h │ ├── common.cpp │ ├── common.h │ ├── logger.h │ ├── main.cpp │ ├── trim.cpp │ └── trim.h ├── bwa │ ├── COPYING │ ├── ChangeLog │ ├── Makefile │ ├── NEWS.md │ ├── QSufSort.c │ ├── QSufSort.h │ ├── README-alt.md │ ├── README.md │ ├── bamlite.c │ ├── bamlite.h │ ├── bntseq.c │ ├── bntseq.h │ ├── bwa.1 │ ├── bwa.c │ ├── bwa.h │ ├── bwakit │ │ ├── README.md │ │ ├── bwa-postalt.js │ │ ├── run-HLA │ │ ├── run-bwamem │ │ ├── run-gen-ref │ │ ├── typeHLA-selctg.js │ │ ├── typeHLA.js │ │ └── typeHLA.sh │ ├── bwamem.c │ ├── bwamem.h │ ├── bwamem_extra.c │ ├── bwamem_pair.c │ ├── bwape.c │ ├── bwase.c │ ├── bwase.h │ ├── bwaseqio.c │ ├── bwashm.c │ ├── bwt.c │ ├── bwt.h │ ├── bwt_gen.c │ ├── bwt_lite.c │ ├── bwt_lite.h │ ├── bwtaln.c │ ├── bwtaln.h │ ├── bwtgap.c │ ├── bwtgap.h │ ├── bwtindex.c │ ├── bwtsw2.h │ ├── bwtsw2_aux.c │ ├── bwtsw2_chain.c │ ├── bwtsw2_core.c │ ├── bwtsw2_main.c │ ├── bwtsw2_pair.c │ ├── example.c │ ├── fastmap.c │ ├── is.c │ ├── kbtree.h │ ├── khash.h │ ├── kopen.c │ ├── kseq.h │ ├── ksort.h │ ├── kstring.c │ ├── kstring.h │ ├── ksw.c │ ├── ksw.h │ ├── kthread.c │ ├── kvec.h │ ├── main.c │ ├── malloc_wrap.c │ ├── malloc_wrap.h │ ├── maxk.c │ ├── pemerge.c │ ├── qualfa2fq.pl │ ├── rle.c │ ├── rle.h │ ├── rope.c │ ├── rope.h │ ├── utils.c │ ├── utils.h │ └── xa2multi.pl ├── delta2pseudo │ ├── Makefile │ ├── base_caller.cc │ ├── base_caller.h │ ├── fa.cc │ ├── fa.h │ ├── hoge.cc │ ├── hoge.h │ └── main.cc ├── fa2snp │ ├── Makefile │ ├── fuga.cc │ ├── fuga.h │ ├── hoge.cc │ ├── hoge.h │ └── main.cc ├── mask_region │ ├── Makefile │ ├── fuga.cc │ ├── fuga.h │ ├── hoge.cc │ ├── hoge.h │ └── main.cc ├── merge_fa │ ├── Makefile │ ├── fuga.cc │ ├── fuga.h │ ├── hoge.cc │ ├── hoge.h │ └── main.cc ├── merge_region │ ├── Makefile │ ├── fuga.cc │ ├── fuga.h │ ├── hoge.cc │ ├── hoge.h │ └── main.cc ├── sam2fq │ ├── Makefile │ ├── fuga.cc │ ├── fuga.h │ ├── hoge.cc │ ├── hoge.h │ └── main.cc ├── sam2pseudo │ ├── Makefile │ ├── fuga.cc │ ├── fuga.h │ ├── hoge.cc │ ├── hoge.h │ ├── main.cc │ ├── sam_l.cc │ └── sam_l.h └── snp2fa │ ├── Makefile │ ├── fuga.cc │ ├── fuga.h │ ├── hoge.cc │ ├── 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