Replace "Short" CIGAR in SA tag with "Full Length" CIGAR? #287
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This will break existing consumers of the SA tag. It must be controlled by a toggle. |
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I agree with you. A toggle is needed. |
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SA is not designed for that purpose. I have to decline the PR. Sorry. |
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Hi Heng,
I'm trying to compute segment mapping identity(both blast identity and Gap-compressed identity) from SA tag. However, I noticed that the CIGAR string in SA tag is in a "Short" format, which make it hard to compute alignment columns, INS size, DEL size and gap open number.
So I replace "Short" CIGAR in SA tag with "Full Length" CIGAR in this commit.
Ignore this pull request if you consider the "Short" one is better.