#105 staden-io-lib: fix io_lib/bam.c read

[Anibal Monsalve Salazar]

Date: Mon, 31 Mar 2014 19:22:13 +0200
From: Aleksandar Zlicic Aleksandar.Zlicic@imgtec.com
Subject: staden-io-lib: fix io_lib/bam.c read

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=736565

We have fixed a bug reported for the staden-io-lib package
(https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=736565). The cause
of this problem is an error in function bam_get_seq(), or to be more
precise, function's implementation for non-intel architectures.

Function bam_get_seq is used for reading data from alignment blocks in
BAM files, block by block.

In special cases, when the alignment block being read is the last
block in BAM file, and the block has no cigar operations and segment
sequence stored inside of it, function incorrectly detects
end-of-file.

In that case, block has actually been successfully read, but because
of erroneous end-of-file detection, it isn't written to output file in
SAM format.

Attached patch fixes this issue.

[James Bonfield]

Argh 5 mins to fix, 30 mins wrestling with SF Allura interface.

I'll cut it short this time (it's eaten 2 replies already)...

Thanks greatly. Now fixed.

James