Cram file input 'Unkown sort order'
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jkbonfield
I was redirected ro rasing this issue here, original query on biobambam2#15
When using bamdownsamplerandom (biobambam2) with cram input the following message is raised:
$ samtools-1.2 view -H cram/MD5146a.cram | head -n 1 @HD VN:1.5 SO:coordinate $ biobambam2-2.0.33-release-20160317091357-x86_64-etch-linux-gnu/bin/bamdownsamplerandom reference=/nfs/cancer_ref01/mouse/37/genome.fa p=0.1 filename=cram/MD5146a.cram inputformat=cram outputformat=cram O=ds.cram Unknown sort order field: unknown ...
Regads,
Keiran
A valid problem. I silenced it with my latest commit by adding "unknown" as a legal term:
Perhaps I’m confused, but where does the unknown come from? The input shows as coordinate sorted in the header.
Thanks,
Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute
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Related
Bugs:
#108I've no idea on that. I assume it's whatever biobambam is doing to the file.
The header parsing code is simply reading in whatever it finds in the header.
If I make a test case with SO:unknown I got the warning, but with the patch it goes away. Why the SO is even there is baffling to me I'm afraid.