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#34 support additional SAM flags
open
nobody
None
5
2009-11-11
2009-11-11
Anonymous
No
SAM Format Specification provides for many additional FLAGs. (.c.f. http://samtools.sourceforge.net/SAM1.pdf\)
It would be great to be able to specify which fields bowtie should produce (perhaps from a limited range), with the understanding that it might increase complexity of computation.
Of paricular interest to me is the IH flag, which I understand to be relevant for the number of loci to which a read maps.
For instance providing bowtie options of --samFlag H0,IH would generate these additional tags
H0 i Number of perfect hits
IH i Number of stored alignments in SAM that contains the query in the current record
Any hope for such?
--Malcolm Cook