Error in htseq-count. Large gaps in CIGAR string

[usha]

Hi,

I am getting this error when I run htseq-count (version 0.5.4p3)

Error occured in line 6684695 of file OUT.gsnap.combined.Control_72_Rep3_R1.fastq.uniq.
Error: value too large to convert to int
[Exception type: OverflowError, raised in _HTSeq.pyx:1120]

The corresponding line in the input file is

HISEQ:488:C3W46ACXX:4:2111:4082:52860 83 Chr08 6311469 40 28S2M4294966387N45M25S = 63083
37 -3002 GAAAATTGAGGATGACTTAGAGGTCTCAAGATCGGCAATGCATCTGGAAAGAAGTGGATATCAATGACTAATGAGGAGAAGGTTAAATACTAT
GATATAG DDDC@CCA>3FFFFFFFHFHEHHEEEEHF;;--0/9AEJIIIIH@GDJHHGJJIIHGHCJHGIIIHFEHHHEHEHIHGIIHEIIJIHDHFFHFFFFF@@@MD:Z:4T42 NH:i:1 HI:i:1 NM:i:1 SM:i:40 XQ:i:40 X2:i:0 XO:Z:CU XS:A:+

I noticed that there is a very large gap in the CIGAR string. I used GSNAP to generate the alignments.

Has anyone encountered this before?

Thanks for your help

[Brian Bushnell]

Looks like a bug in gsnap; you should report it. Then remove that read.