[Feature request] use the input reference genome for CRAM input

[Han-Cao]

Hi,

Thanks for developing this great tool!

I am using trgt 1.5.1-045e37aa. When the input alignment file is CRAM, it seems that TRGT always use the reference genome defined in the CRAM header to decode the reads. This can cause error when pbmm2 and TRGT running on different severs, where TRGT cannot find the path to reference genome.

Many tools use the given reference genome to decode CRAM files (such as samtools --reference), could TRGT also support this feature? TRGT already requires the input reference genome to be the same as alignment, so I think this may not introduce another issue.

-g, --genome Path to the FASTA file containing reference genome. This must be the same reference genomes as the one used for read alignment.

Thanks.

[egor-dolzhenko]

Thank you for letting us know about this issue. We'll add it to our development roadmap.