Pysam does not allow index without ".bam" component.

quachtina96 / pysam

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Pysam does not allow index without ".bam" component. #116

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago

Pysam requires that the index for the file X.bam is named X.bam.bai, unlike 
e.g. samtools which also accepts an index with the filename X.bai. 

This is problematic since some tools (e.g. Picard tools) and some projects 
(e.g. the 1000 Genomes Project) consistently make use of the shorter filename 
for the bai file.

Original issue reported on code.google.com by Mikkel...@gmail.com on 13 Mar 2013 at 2:11

GoogleCodeExporter commented 9 years ago

Thanks, great suggestion.

Added!

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 26 Jun 2013 at 9:05

Changed state: Fixed

GoogleCodeExporter commented 9 years ago

Issue 145 has been merged into this issue.

Original comment by andreas....@gmail.com on 27 Nov 2013 at 8:31

GoogleCodeExporter commented 9 years ago

Is this fixed?

Original comment by margho...@binatechnologies.com on 27 Nov 2013 at 8:54