Depad2 #11
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Depad2 #11
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…le in a padded reference
Note does not (yet) preserve additional @sq line tags (e.g. AS, SP, UR).
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Hi Heng,
This is a replacement/update for #6
I've worked on the handling of superfluous CIGAR P operators in 'samtools depad', and found and fixed a buffer overflow when CIGAR D operators are used.
I also realized you were right originally not to accept CIGAR P operators in the input padded reference BAM file (much like it does not make sense to use CIGAR I in this case either), and restored that check.
The command line API has been extended to support SAM or BAM for input or output, and you can (and should) provide a padded reference FASTA file.
Provided a padded reference FASTA file is provided, the reference lengths in the header (including the @sq lines in the SAM header) are updated. If not, a warning is given. My preferred way to deal with this is to use any embedded references, which requires enhancements to the BAI file (see mailing list). Otherwise a pre-scan of the file could be made to find the embedded references.
Peter