In align_and_count, change default to count only properly-paired reads#534
Open
In align_and_count, change default to count only properly-paired reads#534
Conversation
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`.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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.