BAM fetch requires an index, even when only sequential access is required

MaciekAber / pysam

Automatically exported from code.google.com/p/pysam

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BAM fetch requires an index, even when only sequential access is required #27

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago

Currently, iterating through a BAM file request an index, since the
bam_fetch function is used.  However, is it not always convenient to create
an index file and iteration should still be possible, especially when a
region is not specified.  I also suspect that pure sequential iteration
will be faster using the lower-level APIs like bam_read1 directly.

Original issue reported on code.google.com by bioinformed@gmail.com on 16 Apr 2010 at 1:11

Merged into: #23

GoogleCodeExporter commented 8 years ago

I have this fixed in my local branch, as well as a number of other 
improvements.  I'll 
send these on to the pysam authors.

Original comment by bioinformed@gmail.com on 30 Apr 2010 at 11:16

GoogleCodeExporter commented 8 years ago

Original comment by andreas....@gmail.com on 4 May 2010 at 9:22

Changed state: Duplicate

GoogleCodeExporter commented 8 years ago

Original comment by andreas....@gmail.com on 4 May 2010 at 9:25