htseq count missing last mapped fragment

[mapardo]

I am using the program htseq-count v0.5.3 with an standard sam file from the mapping of a set of paired end reads. Comparing this file with the output file that can be obtained with the option '-o', I've realized that the mapping for the last fragment (two lines) is missing. Furthermore, I check the resulting count and one mapping is missing as well.

Has anybody got the same results? Is there any fix to solve this?

Thank you.

[Simon Anders]

I am using the program htseq-count v0.5.3 with an standard sam file from the mapping of a set of paired end reads. Comparing this file with the output file that can be obtained with the option '-o', I've realized that the mapping for the last fragment (two lines) is missing. Furthermore, I check the resulting count and one mapping is missing as well.

This is a bug, which I fixed a few months ago, in version 0.5.3p1. (Thanks go to Justin Powell who noticed the bug first and even sent me a patch.)

[mapardo]

Sorry. I didnt realize that I was using a version that wasnt updated. Thank you both.