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#22 new CIGAR code 'X'

--
open
nobody
None
False
5
2013-12-05
2013-06-25
No

--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 --

Discussion

  • ian rabe

    ian rabe - 2013-08-26

    Hi,

    I have the same Error, with a .sam file generated by CRAC software too.

    Ian

     
  • Simon Anders

    Simon Anders - 2013-12-05

    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.

     

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