-L chr1 runs but does not output anything

ssadedin / bazam

A read extraction and realignment tool for next generation sequencing data

GNU Lesser General Public License v2.1

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Open bwlang opened 5 years ago

bwlang commented 5 years ago

Thanks for writing this helpful software!

I think it should just extract chr1 reads or fail (reporting an invalid -L argument) Using -L chr1:1-248956422 does work

Npaffen commented 1 year ago

Fully agree here. The tool should extract the contig length itself if it want to be a smooth "bam to bam" pipeline.