bamdownsamplerandom - sort order issues with cram input

[keiranmraine]

Hi,

This gives warnings that the sort order is unknown on files where the field is appropriately set in the header:

$ 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
...

This doesn't occur for BAM input.

Regards, Keiran

[gt1]

Hi Keiran,

this message originates from io_lib. Please create a ticket at https://sourceforge.net/p/staden/bugs/ to have this checked.

Best, German

[keiranmraine]

Raised