[Htseq-general] Bug fix fork of HTSeq

[David L. <da...@gm...>]

Hi guys, I really like HTSeq!

I found a few bugs, and sent them to the maintainer a few weeks ago
but have heard no response (holidays? Changed labs?)

I've put up a fork of the SVN code base here, until the patches are
put into the main branch:

https://bitbucket.org/sacgf/htseq


New Features:

htseq-count works with bam files
Wrote htseq-count-combine.py to merge multiple htseq-count outputs to
one big CSV file

Bug Fixes:

GFF Fix by David Eccles (gringer) on this mailing list
Fixed extend_to_include and GenomicInterval_from_directional attribute errors
Single ended bam files had paired_end incorrectly set
Sam/Bam mate start chrom incorrect default