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Legacy tickets migrated from the OBF Redmine issue tracker: http://redmine.open-bio.org
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bam assys: no sequence in opposite oriented reads #83

Open cjfields opened 8 years ago

cjfields commented 8 years ago

Author Name: Mark A. Jensen (Mark A. Jensen) Original Redmine Issue: 3088, https://redmine.open-bio.org/issues/3088 Original Date: 2010-06-01 Original Assignee: Mark A. Jensen

from Jiri Stiller:

I am trying to process bam file using Bio::Assembly::IO. I attached test script and output. When I am retrieving contigs I get correct contig number and position but contig objects build from reads of different orientation don’t contain any read sequences. Contigs built from the reads of the same orientations are fine.

cjfields commented 8 years ago

Original Redmine Comment Author Name: Mark A. Jensen Original Date: 2010-06-01T12:34:29Z

Created an attachment (id=1509) script reproducing bug with attached data

cjfields commented 8 years ago

Original Redmine Comment Author Name: Mark A. Jensen Original Date: 2010-06-01T12:34:59Z

Created an attachment (id=1510) attached data

cjfields commented 8 years ago

Original Redmine Comment Author Name: Mark A. Jensen Original Date: 2010-06-01T12:35:26Z

Created an attachment (id=1511) output in error

cjfields commented 8 years ago

Original Redmine Comment Author Name: John Anderson Original Date: 2010-07-20T23:25:10Z

Hi, I started looking at this tonight, and it looks like the BAM file referenced in the first attachment (“KBrB056G23_vs_Bna_03_002_paired.bam”) wasn’t uploaded. Could you add that? That way I can replicate the problem as a first step towards trying to fix it.

thanks!

cjfields commented 8 years ago

Original Redmine Comment Author Name: Chris Fields Original Date: 2010-10-11T14:23:51Z

Mark, do we have a representative BAM file for this bug? Otherwise we’ll have to close it out or find another set of data to check this against…

cjfields commented 8 years ago

Original Redmine Comment Author Name: Mark A. Jensen Original Date: 2010-10-11T23:52:48Z

This bug is real. I’m on the case.

cjfields commented 8 years ago

Original Redmine Comment Author Name: Mark A. Jensen Original Date: 2010-10-12T00:57:06Z

Found and fixed it. Look for a push soon.

cjfields commented 8 years ago

Original Redmine Comment Author Name: Jason Stajich Original Date: 2011-03-08T23:50:23Z

Mark is this fixed/pushed in?