new CIGAR code 'X'
Analysing high-throughput sequencing data with Python
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sanders_muc
--Hi,
i think htseq-count doesn't understand the new CIGAR operators X and =
I have this error when reading a sam file with htseq-count (0.5.4p3):
Error occured when reading first line of sam file.
Error: ("Unknown CIGAR code 'X' encountered.", 'line 29 of file AB.sam'
[Exception type: ValueError, raised in _HTSeq.pyx:1163]
(AB.sam is generated by CRAC software)
Laurent --
Hi,
I have the same Error, with a .sam file generated by CRAC software too.
Ian
Sorry for not replying earlier.
This "X" CIGAR operation is a new addition to the SAM specification, which was (as usual, unfortunately) silently added to the spec (which lacks proper versioning). We have a bit a hard time keeping up with these changes.
I've filed this as bug #16 to remind us to add support for it in the next release.