Cram support

[JosephLalli]

Hi there,

I'm trying to get your tool up and running, and I've managed to get it to compile. However, I'm having difficulty working with cram files.

When running extractHAIRS I'm seeing the error message:

reading sorted bamfile hapcut2_testing/672_D1.gatk.grch38.cram
unable to load bam index for file hapcut2_testing/672.cram 

Bam files are working well.

Is this working as expected?

Thanks,
Joe

[vibansal]

The tool did not support cram files until now. The code has been updated to handle cram files (see latest commit). Thanks for pointing this out. Let me know if you encounter any errors.