htslib 0.1.0 → 0.2.2
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- checksums.yaml +4 -4
- data/README.md +30 -11
- data/lib/hts/bam/aux.rb +1 -0
- data/lib/hts/bam/cigar.rb +5 -7
- data/lib/hts/bam/flag.rb +5 -0
- data/lib/hts/bam/header.rb +1 -0
- data/lib/hts/bam/record.rb +7 -4
- data/lib/hts/bam.rb +128 -35
- data/lib/hts/bcf/format.rb +4 -4
- data/lib/hts/bcf/header.rb +1 -0
- data/lib/hts/bcf/header_record.rb +11 -0
- data/lib/hts/bcf/info.rb +3 -2
- data/lib/hts/bcf/record.rb +31 -30
- data/lib/hts/bcf.rb +183 -30
- data/lib/hts/faidx.rb +62 -21
- data/lib/hts/hts.rb +54 -2
- data/lib/hts/libhts/bgzf.rb +5 -5
- data/lib/hts/libhts/constants.rb +42 -20
- data/lib/hts/libhts/cram.rb +312 -279
- data/lib/hts/libhts/hfile.rb +29 -11
- data/lib/hts/libhts/hts.rb +158 -25
- data/lib/hts/libhts/sam.rb +695 -94
- data/lib/hts/libhts/sam_funcs.rb +131 -588
- data/lib/hts/libhts/tbx.rb +1 -1
- data/lib/hts/libhts/tbx_funcs.rb +25 -0
- data/lib/hts/libhts/vcf.rb +460 -234
- data/lib/hts/libhts/vcf_funcs.rb +277 -424
- data/lib/hts/libhts.rb +1 -0
- data/lib/hts/tbx.rb +39 -8
- data/lib/hts/version.rb +1 -1
- metadata +5 -3
data/lib/hts/libhts/tbx.rb
CHANGED
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@@ -0,0 +1,25 @@
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module HTS
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module LibHTS
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class << self
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def tbx_itr_destroy(iter)
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hts_itr_destroy(iter)
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end
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def tbx_itr_queryi(tbx, tid, beg, end_)
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hts_itr_query(tbx[:idx], tid, beg, end_, tbx_readrec)
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end
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def tbx_itr_querys(tbx, s)
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hts_itr_querys(tbx[:idx], s, @@tbx_name2id, tbx, @@hts_itr_query, @@tbx_readrec)
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end
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def tbx_itr_next(htsfp, tbx, itr, r)
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hts_itr_next(hts_get_bgzfp(htsfp), itr, r, tbx)
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end
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def tbx_bgzf_itr_next(bgzfp, tbx, itr, r)
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hts_itr_next(bgzfp, itr, r, tbx)
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end
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end
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end
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end
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