hall-lab/extract_sv_reads: extract-sv-reads v1.2.0

This release introduces some speed improvements for both BAM and CRAM file inputs. Threading now affects the processing of BAMs as well as CRAMs. File writing is now multi-threaded (in addition to file reading) and thus the threading option naming has changed to reflect that. Switch any scripts to use --threads instead of --input-threads. Only the information needed to produce the splitters and discordants files are read from the CRAM. This means that the MD tag is no longer generated and written in the output. It also means significant speed improvements (in our testing ~2x) when reading a CRAM file and writing out BAMs that don't contain sequence or quality fields.

Related Organizations

University of Mary
United States

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