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