Feature request: Add option for reference to cluster_identifier

[nvnieuwk]

Hi,

Is it possible to add the option to specify the reference file in cluster_identifier? I'm trying to run it using a CRAM file and the tool looks for the reference but can't find it automatically.

Or do you know of a way I can specify this myself?

Thanks
-Nicolas

[nvnieuwk]

Adding this before executing cluster_identifier worked for me:

wget https://raw.githubusercontent.com/samtools/samtools/master/misc/seq_cache_populate.pl 
perl seq_cache_populate.pl -root ./md5_ref $fasta 
export REF_PATH=`pwd`/md5_ref/%2s/%2s/%s

[nvnieuwk]

This seems like a bit of a sketchy work around though. It would still be nice if you could add a --reference argument to the tool. Thanks!