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guanchangge / mosaik-aligner

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The generated .multiple.bam file is not valid BAM. #116

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
1. run Mosaik

What is the expected output? What do you see instead?

Expected output is to get two BAM files, one for unique (?) alignments, one for 
multiple ones. Both should be valid BAM files. The one for multiple alignments 
cannot be read by samtools, it segfaults. My own BAM reader library reports 
problems reading the header.

What version of the product are you using? On what operating system?

Both 2.1.33 and the current git version.

Original issue reported on code.google.com by zyklenf...@gmail.com on 9 Feb 2012 at 8:12

GoogleCodeExporter commented 8 years ago 
All alignments (including unique, multiple, and unmapped) are kept in 
<NAME>.bam.

The multiple.bam actually is like a mapping distribution. Once we got multiple 
mappings for a mate/read, we record the chromosome ids and positions of them in 
multiple.bam. More precisely, if -om is not enabled, only chromosome ids and 
positions are shown in multiple.bam. bamtools 
(https://github.com/pezmaster31/bamtools) can handle that bam.

Original comment by WanPing....@gmail.com on 9 Feb 2012 at 3:36