Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Added support for bwa-mem2 to the CPU version to speedup the alignmen… #360

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Added support for bwa-mem2 to the CPU version to speedup the alignmen… #360

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 12 additions & 3 deletions CPU/juicer.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -262,10 +262,19 @@ then
fi

## Check that index for refSeq exists
if [[ ! -e "${refSeq}.bwt" ]]
if [[ ! -e "${refSeq}.bwt.2bit.64" ]]
then
echo "***! Reference sequence $refSeq does not appear to have been indexed. Please run bwa index on this file before running juicer.";
exit 1;
echo "bwa-mem2 index was not found. Checking if bwa index exists...";
if [[ ! -e "${refSeq}.bwt" ]]
then
echo "***! Reference sequence $refSeq does not appear to have been indexed. Please run 'bwa index' or 'bwa-mem2 index' on this file before running juicer.";
exit 1;
fi
echo "bwa index was found. Using...";
bwa_cmd="bwa";
else
echo "bwa-mem2 index was found. Using...";
bwa_cmd="bwa-mem2";
fi
fi

Expand Down