├── .gitignore ├── README.md ├── fqs ├── application.cpp ├── application.h ├── bit_vec.h ├── code_ctx.cpp ├── code_ctx.h ├── compressor.cpp ├── compressor.h ├── context_hm.h ├── defs.h ├── dna.cpp ├── dna.h ├── fqs.vcxproj ├── fqs.vcxproj.filters ├── fqs.vcxproj.user ├── fqsqueezer.cpp ├── ht_kmer.cpp ├── ht_kmer.h ├── id.cpp ├── id.h ├── io.h ├── kmer.h ├── libs │ ├── Debug │ │ └── zlibstat.lib │ ├── Release │ │ └── zlibstat.lib │ ├── libz.a │ ├── zconf.h │ ├── zlib.h │ └── zlibstat.lib ├── meta.cpp ├── meta.h ├── mtf.cpp ├── mtf.h ├── params.h ├── quality.cpp ├── quality.h ├── queue.h ├── rc.h ├── reads_block.h ├── sub_rc.h ├── utils.cpp └── utils.h ├── fqsqueezer.sln └── makefile /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/README.md -------------------------------------------------------------------------------- /fqs/application.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/application.cpp -------------------------------------------------------------------------------- /fqs/application.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/application.h -------------------------------------------------------------------------------- /fqs/bit_vec.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/bit_vec.h -------------------------------------------------------------------------------- /fqs/code_ctx.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/code_ctx.cpp -------------------------------------------------------------------------------- /fqs/code_ctx.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/code_ctx.h -------------------------------------------------------------------------------- /fqs/compressor.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/compressor.cpp -------------------------------------------------------------------------------- /fqs/compressor.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/compressor.h -------------------------------------------------------------------------------- /fqs/context_hm.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/context_hm.h -------------------------------------------------------------------------------- /fqs/defs.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/defs.h -------------------------------------------------------------------------------- /fqs/dna.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/dna.cpp -------------------------------------------------------------------------------- /fqs/dna.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/dna.h -------------------------------------------------------------------------------- /fqs/fqs.vcxproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/fqs.vcxproj -------------------------------------------------------------------------------- /fqs/fqs.vcxproj.filters: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/fqs.vcxproj.filters -------------------------------------------------------------------------------- /fqs/fqs.vcxproj.user: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/fqs.vcxproj.user -------------------------------------------------------------------------------- /fqs/fqsqueezer.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/fqsqueezer.cpp -------------------------------------------------------------------------------- /fqs/ht_kmer.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/ht_kmer.cpp -------------------------------------------------------------------------------- /fqs/ht_kmer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/ht_kmer.h -------------------------------------------------------------------------------- /fqs/id.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/id.cpp -------------------------------------------------------------------------------- /fqs/id.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/id.h -------------------------------------------------------------------------------- /fqs/io.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/io.h -------------------------------------------------------------------------------- /fqs/kmer.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/kmer.h -------------------------------------------------------------------------------- /fqs/libs/Debug/zlibstat.lib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/libs/Debug/zlibstat.lib -------------------------------------------------------------------------------- /fqs/libs/Release/zlibstat.lib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/libs/Release/zlibstat.lib -------------------------------------------------------------------------------- /fqs/libs/libz.a: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/libs/libz.a -------------------------------------------------------------------------------- /fqs/libs/zconf.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/libs/zconf.h -------------------------------------------------------------------------------- /fqs/libs/zlib.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/libs/zlib.h -------------------------------------------------------------------------------- /fqs/libs/zlibstat.lib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/libs/zlibstat.lib -------------------------------------------------------------------------------- /fqs/meta.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/meta.cpp -------------------------------------------------------------------------------- /fqs/meta.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/meta.h -------------------------------------------------------------------------------- /fqs/mtf.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/mtf.cpp -------------------------------------------------------------------------------- /fqs/mtf.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/mtf.h -------------------------------------------------------------------------------- /fqs/params.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/params.h -------------------------------------------------------------------------------- /fqs/quality.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/quality.cpp -------------------------------------------------------------------------------- /fqs/quality.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/quality.h -------------------------------------------------------------------------------- /fqs/queue.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/queue.h -------------------------------------------------------------------------------- /fqs/rc.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/rc.h -------------------------------------------------------------------------------- /fqs/reads_block.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/reads_block.h -------------------------------------------------------------------------------- /fqs/sub_rc.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/sub_rc.h -------------------------------------------------------------------------------- /fqs/utils.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/utils.cpp -------------------------------------------------------------------------------- /fqs/utils.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqs/utils.h -------------------------------------------------------------------------------- /fqsqueezer.sln: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/fqsqueezer.sln -------------------------------------------------------------------------------- /makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/refresh-bio/fqsqueezer/HEAD/makefile --------------------------------------------------------------------------------