421 Commits (master)
 

Author SHA1 Message Date
lomereiter 3343c66e08 support for gzipped SAM by piping `gunzip -c` 9 years ago
lomereiter 1560f69119 faster BAM reading 9 years ago
lomereiter 706d11a3b4 removed unused code 9 years ago
lomereiter 919d901c46 replaced File.byLine with ByLineFast 9 years ago
lomereiter 06838b1339 more idiomatic SAM reading 9 years ago
lomereiter 52d0ae3ce7 better SAM parser 9 years ago
lomereiter 36f00232c2 added finishFunc param to readsWithProgress 9 years ago
lomereiter d6fc2a064b Merge branch 'master' of git://github.com/biod/BioD 9 years ago
Artem Tarasov 4f967c5902 avoid unnecessary allocations when outputting BGZF 9 years ago
lomereiter 88801851f7 Merge branch 'master' of git://github.com/biod/BioD 9 years ago
lomereiter 01cec5ec16 new BamRead properties 9 years ago
lomereiter 65c9914843 removed BS 9 years ago
Artem Tarasov 994eed949a revert commit e53af 9 years ago
lomereiter 37552a3b31 Merge branch 'master' of git://github.com/biod/BioD 9 years ago
lomereiter 8f88b4d0ab unittests run successfully on winxp; closes #1 9 years ago
lomereiter 611621e998 (WIP) windows support #1 9 years ago
lomereiter e53af29402 replaced dump algo of getting bins for region 9 years ago
lomereiter 7ad037bcb4 store source range in pileup instance 9 years ago
lomereiter 7cd5203431 store source read range in pileup instance 9 years ago
Artem Tarasov d2bea0a0da a few fixes to get maq caller working again 9 years ago
Artem Tarasov deb90bdad1 fix 9 years ago
lomereiter a290e05360 added bio.bam.pileup.useMD for clarity 9 years ago
lomereiter 57c81f275f changed license to MIT 9 years ago
lomereiter 703c0847c6 fixed index creation behaviour 9 years ago
lomereiter 6b128a7998 DMD optimizer seems to incorrectly handle properties 9 years ago
lomereiter dd1f38682e [pileup] optionally skip sites with zero coverage 9 years ago
lomereiter 37ed738d79 fixes for 2.063; also fixed tag value typeids 9 years ago
lomereiter 32fb5a45a4 new BamRead method: extended_cigar 9 years ago
lomereiter 73de9f25d9 check CIGAR length to fit in ushort type 9 years ago
Artem Tarasov 29f2d91ad7 make lib compilable with LDC trunk 9 years ago
lomereiter d109ffc384 fixed a bug in bio.bam.writer 9 years ago
lomereiter 6d5899ebde simple MAF parser 9 years ago
Artem Tarasov ac1eb8510e a few improvements 9 years ago
lomereiter 7a41ba7b00 refactored random access a bit 9 years ago
lomereiter 9d4ef7ca9d multiple BAM reader (2.061+) 9 years ago
lomereiter 6485fe1deb msgpack output for header 9 years ago
lomereiter 0d7250b897 SAM header JSON formatting 9 years ago
lomereiter 9143bf6978 updated example 6 9 years ago
lomereiter 73da46c93e new awesome serialization to sam/json 9 years ago
lomereiter d973b805c0 throw exceptions in case of file reading problems 9 years ago
lomereiter 996e4b1a3b fix const in json serialization 9 years ago
lomereiter 35e48e197f EAGAIN/EWOULDBLOCK handling 9 years ago
lomereiter 02ad9dff11 faster BamRead.toString 9 years ago
lomereiter 2ecabe69c5 fixes in Value.toString 9 years ago
lomereiter bf12b493f4 implemented idiomatic toString for BamRead 9 years ago
lomereiter 515f9718ea bio.bam.reader docs: intro with examples 9 years ago
lomereiter ee7fbab192 further documentation improvements 9 years ago
lomereiter 24474ac73b improving docs... 9 years ago
lomereiter ef648ee005 improved bio.bam.writer and bio.bam.pileup docs 9 years ago
lomereiter c04c314104 improved bio.bam.reader docs 9 years ago