Add function cram_encoder_get_fd in cram_bambam.[ch]

jkbonfield / io_lib

Staden Package "io_lib" (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats.

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Add function cram_encoder_get_fd in cram_bambam.[ch] #27

Closed gt1 closed 4 years ago

gt1 commented 4 years ago

Hello James,

here is a patch for your consideration. It essentially adds a new function cram_encoder_get_fd to obtain a cram_fd pointer from an encoding context for bambam. This is necessary to access the new encoding profile setting interface. The patch also moves the encoding interface to a separate file (cram_bambam.h).

Best, German

jkbonfield commented 4 years ago

Apologies for forgetting about this PR. It's a reasonable change and I'm happy to assist biobambam, which ultimately is the only thing affected by these changes anyway.

gt1 commented 4 years ago

Thanks a lot for including this. I had someone asking whether bamsormadup could be changed to directly produce archive mode cram files and this is now possible.

Best wishes German