broadinstitute / viral-pipelines

viral-ngs: complete pipelines
Other
60 stars 28 forks source link

In align_and_count, change default to count only properly-paired reads #534

Open tomkinsc opened 6 months ago

tomkinsc commented 6 months ago

Change the input, filter_bam_to_proper_primary_mapped_reads, in align_and_count to a default value of true; this changes the behavior of the task. Before filtering was available as an optional operation in align_and_count, reads were not filtered to proper pairs and later on the value of filter_bam_to_proper_primary_mapped_reads=false maintained the no-filter approach. With this commit, only properly-paired mapped reads are counted in align_and_count.