Does cramino support unmapped bam?

wdecoster / cramino

A *fast* tool for BAM/CRAM quality evaluation, intended for long reads

MIT License

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Does cramino support unmapped bam? #15

Closed ymcki closed 1 year ago

ymcki commented 1 year ago

It works with the cram file I have but crashes when I give it an unmapped bam:

~/utils/cramino -t 4 ABC.ubam --arrow ABC.unmapped.feather File name ABC.ubam [2023-07-21T04:19:31Z ERROR cramino] Not enough reads to calculate metrics! thread 'main' panicked at 'explicit panic', src/main.rs:155:9 note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

By the way, is it possible to also output number of mapped bases and unmapped bases for aligned cram/bam?

wdecoster commented 1 year ago

Indeed, cramino does not support ubam (for now). I will think about your other suggestion regarding number of (un)mapped bases.

wdecoster commented 1 year ago

Cramino v0.10.0 has support for ubam files, with --ubam. The number of mapped bases is not yet supported and more likely would be provided as the fraction of mapped reads in a future version.