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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Only include paired-end sequencing reads in discordants file #279

Closed ernfrid closed 5 years ago

ernfrid commented 5 years ago

I've encountered a few CRAMs in the wild where there are reads that aren't from paired-end sequencing runs. These did not have the BAM_FMUNMAP bit set so I've added a check that the sequencing run was paired to the section writing to the discordants file.

I also reindented to remove a bunch of tabs.

I've a test in process and the code change seems to help, but please review critically. cc @brentp @ryanlayer

Thanks!

ernfrid commented 5 years ago

If this looks good, is it possible to merge so I can build against the official repo instead of my fork? Thanks!

brentp commented 5 years ago

CC @ryanlayer @arq5x

ernfrid commented 5 years ago

Thanks @ryanlayer!