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