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Committed 04 Mar 2024 06:59PM UTC coverage: 0.0%. Remained the same

Job # 8145573512.1

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web-flow

Commit Message

add read_utils.py::filter_bam_to_proper_primary_mapped_reads(); add same and expose in minimap2_idxstats and bwamem_idxstats (#91)

* add read_utils.py::filter_bam_to_proper_primary_mapped_reads(); add same and expose in minimap2_idxstats and bwamem_idxstats

add read_utils.py::filter_bam_to_proper_primary_mapped_reads() to remove from a bam file any reads not flagged as being properly paired. This same functionality is added as an optional feature of minimap2_idxstats and bwamem_idxstats if --filterReadsAfterAlignment is specified (preserving the prior functionality for invocations calling these functions the old way, without --filterReadsAfterAlignment)

* add some newlines

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