Eg "samtools view -T human.fa human.cram" but we have a "1" vs "chr1" mix up.
It's not a hard error, as we may have a partial reference we wish to use and there are further fallback measures to continue. Similarly we cannot check this at header loading time, as possibly we have a reference file for a single chromosome, a CRAM aligned against that single chromosome, but all SQ lines present in the header.
Eg "samtools view -T human.fa human.cram" but we have a "1" vs "chr1" mix up.
It's not a hard error, as we may have a partial reference we wish to use and there are further fallback measures to continue. Similarly we cannot check this at header loading time, as possibly we have a reference file for a single chromosome, a CRAM aligned against that single chromosome, but all SQ lines present in the header.
Improves the diagnostics for #1515