ExtractHLAread.sh fails when the input file is in .cram format.

[pjgreer]

If starting from an aligned bam/cram file, ExtractHLAread.sh fails when the file is in .cram format.

The samtools command to extract the HLA regions needs to have the -T reference.fasta flag inserted due to the .cram file compression.

[wshuai294]

Thanks for the feedback! We'll revise it as suggested.

[pjgreer]

OK, you may want to add a flag to the ExtractHLAread.sh to point to the user downloaded ref.fasta The ref.fasta and fai files are over 3GB and you probably should not be distributing them.

haveing the -T ref.fasta flag there for .bam files doesnt hurt anything for .bam file reads, but it must be there for .cram files.

and Thanks for the quick response.