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

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

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15 changes: 12 additions & 3 deletions CPU/juicer.sh
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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

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