error: "could not open input BAM files " when BAM @VN mismatches

ekg / bamaddrg

adds sample names and read-group (RG) tags to BAM alignments

MIT License

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error: "could not open input BAM files " when BAM @VN mismatches #3

Closed mdshw5 closed 9 years ago

mdshw5 commented 9 years ago

I've discovered that bamaddrg fails when presented with one file having @HD VN:1.5 SO:coordinate and the other @HD VN:1.0 SO:coordinate. Is this expected behavior? Is there any reason SAM streams with different version should not be combined?

mdshw5 commented 9 years ago

Hey @ekg. I'll close this issue, since I've figured out my issue. It wasn't actually the VN mismatch, but was actually a single contig that was named differently in either BAM file. I'm still not sure that this should be interpreted as a fatal error, and it seems like the correct behavior would be to merge the @SQ sections of the header as well as the alignments.