Hi John, Yeah, it certainly does contain a lot reference sequences. Sorry should have checked github issues first, but thanks for letting me know. I will continue to use 0.1.19 for sorting until 1.1 comes out.
Cheers, Adam. ________________________________________ From: John Marshall [[email protected]] Sent: Friday, September 05, 2014 8:31 PM To: Adam Skarshewski Cc: [email protected] Subject: Re: [Samtools-help] Samtools sort (merging) is slow On 5 Sep 2014, at 06:52, Adam Skarshewski <[email protected]> wrote: > Running into a problem with samtools 1.0 sort, specifically the merging > phase. It's very slow compared to the previous version. I have a 965MB bam > file (which is already sorted) Does your BAM file have rather a lot of reference sequences? There is a known problem in the new header merging [1] that we are working on fixing, that happens when sorting/merging files mapped to thousands of contigs. John [1] https://github.com/samtools/samtools/issues/260 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
