99 Commits (57c81f275faab5cdec4746bfc7af81e31bac0f69)
 

Author SHA1 Message Date
lomereiter 7847d19753 added Option.mdExtra to basesWith 9 years ago
lomereiter fde3f8232f fixed bio.bam.md.reconstruct.dna 9 years ago
lomereiter aaddb9333c support for options in basesWith 9 years ago
lomereiter 852c1b62e6 fixed unittests by adding opEquals to PerBaseInfo.Result 9 years ago
lomereiter 2933818678 fixes 9 years ago
lomereiter 6dda861117 optional cigar_before/cigar_after in basesWith 9 years ago
lomereiter a9504b2d4d cache MD operation in basesWith iteration 9 years ago
lomereiter b7b1dcfe24 removed unnecessary debug statement 9 years ago
lomereiter 168052e154 added another example on pileup 9 years ago
lomereiter 8907b118ed renamed module pileuprange to pileup 9 years ago
lomereiter a7dd41f09c fix docs 9 years ago
lomereiter 9bcd8285ad updated example of using baseinfo module 9 years ago
lomereiter ec2c9aeb0c basesWith: MD tag 9 years ago
lomereiter 3232ed82ac fix comment 9 years ago
lomereiter a636e10641 . 9 years ago
lomereiter dd5b4a7183 fixes 9 years ago
lomereiter d6fd351a65 example of creating BAM from scratch 9 years ago
lomereiter f4984db147 renames: writeRead -> writeRecord; phred_base_quality -> base_qualities 9 years ago
lomereiter 2fadd7f1ff new BamWriter class; bio.bam.output is deprecated 9 years ago
lomereiter d38d2b17da bgzf input/output streams 9 years ago
lomereiter c83673f747 renamed IChunkInputStream to BgzfInputStream 9 years ago
lomereiter 5f3ba8fd97 . 9 years ago
lomereiter 9218e12a38 moved BGZF-related code to bio.core.bgzf 9 years ago
lomereiter b3f2466d46 fixes; example of iterating several datasets 9 years ago
lomereiter 7781f4aefd less allocations during BAM reading 9 years ago
lomereiter f942aa7f4b license 9 years ago
lomereiter 3b0b17f01c example of working with tags 9 years ago
lomereiter 04ab14fd4f example of getting DNA from MD tags 9 years ago
lomereiter 141596884c fixed a bug in baseinfo.d; added another example 9 years ago
lomereiter 2e269a1fe2 fix bug in random access code 9 years ago
lomereiter a3c14e5b45 example of reading bam and pileup 9 years ago
lomereiter c5711201ff [CigarOperation] renamed operation to type 9 years ago
lomereiter 5ef136fc9d renamed read_name to name 9 years ago
lomereiter 575f57e9e9 provide more information about pileup state 9 years ago
lomereiter 098f567d2b micro optimizations 9 years ago
lomereiter dc7c171abe struggling with DMD inliner dumbness 9 years ago
lomereiter 7ad0d37b78 inputRangeObject sucks (we all <3 inlining!) 9 years ago
lomereiter b7a1cd6bb2 fix 9 years ago
lomereiter bb5a5cbfb0 added public property filename to bam reader 9 years ago
lomereiter 9fdba56fd1 fixes 9 years ago
lomereiter ec3dc0986b changes in basesWith behaviour 9 years ago
lomereiter 0f348e8bb7 made KMer char2code and code2base public static 9 years ago
lomereiter 9c78ed3aa0 added constructor from id to kmer 9 years ago
lomereiter c53374e07b kmer struct 9 years ago
lomereiter c37567fee0 renamed Sam/BamFile to Sam/BamReader and made them classes 9 years ago
lomereiter 6a18d0885b sff 9 years ago
lomereiter da9824be96 make unittests compile with -property 9 years ago
lomereiter b307d0f7be sff reader 9 years ago
lomereiter a1dcb7075e initial commit 9 years ago