Add customizable samtools exclude flag #503
Merged
Conversation
This file contains 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
* Add customizable samtools exclude flag This adds a new parameter, `--samtools_exclude_flags` that allows one to customize which reads are excluded from CRISPRessoWGS and CRISPRessoPooled runs. * Allow for user filtering of reads in Pooled when calculating n_aligned * Add parameter for CRISPRessoCORE to exclude reads * Fix WGS not having access to args * Update pooled samtools exclude flags to be bitwise OR and add unit tests * Point to new test branch * Update help message for samtools_exclude_flags * Move integration test branch back to master
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
This adds a new parameter,
--samtools_exclude_flagsthat allows one to customize which reads are excluded from CRISPRessoWGS and CRISPRessoPooled runs.