Fixed crashing on alignment files without sequence data #113
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romansloutsky wants to merge 2 commits intoyarden:fastmisofrom
romansloutsky:fastmiso
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Fixed crashing on alignment files without sequence data #113romansloutsky wants to merge 2 commits intoyarden:fastmisofrom romansloutsky:fastmiso
romansloutsky wants to merge 2 commits intoyarden:fastmisofrom
romansloutsky:fastmiso
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added 2 commits
September 20, 2017 17:04
Samfile has been deprecated in favor of pysam.AlignmentFile. It's only kept for backwards compatibility.
When an alignment file doesn't contain sequence information, read objects get initialized with read.seq=None (or however that happens in the C code under the hood). In this case len(bam_read.seq) raises an error.
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@yarden #112
While I was at it, I replaced pysam.Samfile with pysam.AlignmentFile everywhere I found it.