removes soft clips before saving as fasta/q#2233
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Hello, when are you planning to release a new version with this feature? |
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We have a couple of pieces of work to finish off before a new release. Hopefully if shouldn't be long. |
Great, thank you for your prompt reply. |
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Fixes #1275
Removes bases corresponding to soft clips. CIGAR and quality values are updated accordingly.
The modified data are stored in aux tags with tag 's0', as 'Z' type array. The aux tag can be controlled with --sc-aux option.
If such aux tag storing is not required, it can be disabled with --no-sc-bkp option.
With reads with reverse flag, the output is reversed and flipped, and the same is done with dumped aux tags as well; the cigar, bases and quality values are reversed and flipped as required.
No other aux tag is updated and at the end of soft clip removal, other aux tag may not be in sync with soft-clipped data if they are about removed data.
Doesn't handle very large cigar tags in bcf aux tag, just uses the cigar in bam.