add command line option --inhibit-vep #1
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
sheridancbio
commented
Apr 6, 2020
sheridancbio
commented
- update docs and README
- update docs and README
ao508
reviewed
Apr 6, 2020
| @@ -528,8 +532,8 @@ sub GetBiotypePriority { | |||
| # one transcript per variant whose annotation will be used in the MAF | |||
| my $maf_fh = IO::File->new( $output_maf, ">" ) or die "ERROR: Couldn't open --output-maf: $output_maf!\n"; | |||
| $maf_fh->print( "#version 2.4\n" . join( "\t", @maf_header ), "\n" ); # Print MAF header | |||
| ( -s $output_vcf ) or exit; # Warnings on this were printed earlier, but quit here, only after a blank MAF is created | |||
| my $annotated_vcf_fh = IO::File->new( $output_vcf ) or die "ERROR: Couldn't open annotated VCF: $output_vcf!\n"; | |||
| ( -s $input_vcf ) or exit; # Warnings on this were printed earlier, but quit here, only after a blank MAF is created | |||
There was a problem hiding this comment.
keep the variable referenced here as output_vcf (remove var name change)
There was a problem hiding this comment.
output file is still expected even if annotation isn't performed
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Outdated suggestions cannot be applied.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.