Closed johnbradley closed 3 years ago
The run-escape-variants.sh script contains a check that the genome file has been setup using setup-escape-variants.sh. This check assumed that bwa idx creates a file with a ".fai" extension. This may not always be the case for bwa.
bwa idx
bwa
Changes here simplify this check to just look for a ".dict" file that is explicitly created by create-picard-dictionary.sh. This is the last step in setup-escape-variants.sh.
Fixes #29
The run-escape-variants.sh script contains a check that the genome file has been setup using setup-escape-variants.sh. This check assumed that
bwa idx
creates a file with a ".fai" extension. This may not always be the case forbwa
.Changes here simplify this check to just look for a ".dict" file that is explicitly created by create-picard-dictionary.sh. This is the last step in setup-escape-variants.sh.
Fixes #29