Query: does bb2 support new bgzip fasta reference?

gt1 / biobambam2

Tools for early stage alignment file processing

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Query: does bb2 support new bgzip fasta reference? #28

Closed keiranmraine closed 8 years ago

keiranmraine commented 8 years ago

I recently tried to convert a BAM to CRAM with scramble providing a bgzip compressed fasta file and index as generated by samtools 1.3+ and found it wasn't compatible.

Is this supported in biobambam2 or would this limitation carry over (from io_lib)?

gt1 commented 8 years ago

biobambam2 relies on io_lib concerning pretty much everything relating to CRAM, so I would expect the limitation to carry over to biobambam2. Maybe James would like to add support for compressed reference files in io_lib.

keiranmraine commented 8 years ago

Currently in discussion, closing.