Make bam_tag2cigar's CG tag handling more lenient. #1317
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The SAM specification explicitly states the type for this tag is CG:B:I. However Htsjdk (sometimes or always?) writes these tags as CG:B:i. Htslib then silently ignores the tag, assuming it's some unofficial (and incorrect) abuse of an uppercase tag for some local purpose. Given that there is data published in the wild using the incorrect data type, it would be less problematic for us to simple handle the incorrect value sign than the minimal risk of misinterpretting someone's private tag data as CIGAR. (Plus they'd bring such woe onto themselves by using the official name-space.) Fixes samtools/samtools#1477 See also samtools/htsjdk#1560
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This seems safe enough. I doubt |
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The SAM specification explicitly states the type for this tag is
CG:B:I. However Htsjdk (sometimes or always?) writes these tags as
CG:B:i. Htslib then silently ignores the tag, assuming it's some
unofficial (and incorrect) abuse of an uppercase tag for some local
purpose.
Given that there is data published in the wild using the incorrect
data type, it would be less problematic for us to simply handle the
incorrect value sign than the minimal risk of misinterpretting
someone's private tag data as CIGAR. (Plus they'd bring such woe onto
themselves by using the official name-space.)
Fixes samtools/samtools#1477
See also samtools/htsjdk#1560