#108 Cram file input 'Unkown sort order'

[Keiran Raine]

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

[James Bonfield]

A valid problem. I silenced it with my latest commit by adding "unknown" as a legal term:

[Keiran Raine]

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

On 24 Mar 2016, at 14:42, James Bonfield jkbonfield@users.sf.net wrote:

A valid problem. I silenced it with my latest commit by adding "unknown" as a legal term:

Attachments:

patch.txt https://sourceforge.net/p/staden/bugs/_discuss/thread/bc69b823/93b3/attachment/patch.txt (464 Bytes; text/plain)
[bugs:#108] https://sourceforge.net/p/staden/bugs/108/ Cram file input 'Unkown sort order'

Status: open
Group: Any
Created: Thu Mar 24, 2016 01:16 PM UTC by Keiran Raine
Last Updated: Thu Mar 24, 2016 01:16 PM UTC
Owner: nobody

I was redirected ro rasing this issue here, original query on biobambam2#15 https://github.com/gt1/biobambam2/issues/15#issuecomment-200537636
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

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/staden/bugs/108/ https://sourceforge.net/p/staden/bugs/108/
To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/ https://sourceforge.net/auth/subscriptions/

--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.

[James Bonfield]

I'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.