Apply m_cram_reference to bams #38
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Yikes, you're right, it seems my test cases first set the CRAM reference so I never noticed this. Thanks for the fix! Not an easy bug to find. |
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See #34
The value of
_Bam::m_cram_referenceis never meaningfully propagated to the underlying htslib bam constructs.If
BamReader::SetCramReferenceis called before any crams are opened,BamReader::m_cram_referenceis never passed to new bams inBamReader::Open, so the new_Bamnever callshtslib::cram_load_reference.This PR adds a single line so that
m_cram_referenceis passed into new bams when opened.This PR does not fix the case where bams have already opened via
BamReader::Openbefore setting a reference. It will probably involve copying this code segment intoBamReader::SetCramReference, but I didn't want to just start duplicating code blocks in case you wanted to move that into it's own function.