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Improve implementation of CRAM support

Open scwatts opened this issue 8 months ago • 2 comments

  • the initial mechanism to support CRAM input has been to simply handle under the internal BAM filetype
  • support for CRAM should be more explicit and be given an internal CRAM filetype instead
  • more generally, inputs of a specific filetype should have some restrictions around file extension

scwatts avatar Apr 04 '25 20:04 scwatts

See commits:

  • f17c17c: Add CRAM/CRAM_REDUX/CRAI filetypes. Internally, these are treated the same as BAM/BAM_REDUX/BAI files
  • 2f928e7: Update docs regarding starting from CRAM, and add warning regarding performance issues with reading small CRAMs

luan-n-nguyen avatar May 27 '25 05:05 luan-n-nguyen

I appreciate the start you've made on this, I'll make some adjustments to generalise the implementation further prior to the 2.2.0 release as planned

scwatts avatar May 27 '25 05:05 scwatts

Marking as complete for now, noting that they may additional improvements in the future

scwatts avatar Aug 25 '25 10:08 scwatts