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Revision as of 11:03, 4 August 2010
, 11:03, 4 August 2010→How would this be used by SamRecord
When SamRecord needs to convert from SAM to BAM or BAM to SAM or needs alignment length or numOverlaps,e tc, it would use the appropriate Cigar::set.
When SamRecord needs to convert from SAM to BAM or BAM to SAM or needs alignment length or numOverlaps,e tc, it would use the appropriate Cigar::set.
The conversion logic and parsing logic SAM & BAM would only be located in this Cigar class.
The conversion logic and parsing logic SAM & BAM would only be located in this Cigar class.
The alignment length calculation would come from the cigar.
What about alignment end (pass in the start position)?
Unclipped Start/End would also be from Cigar - or would it just be offsets - or either depending on whether or not the start pos is passed in.
