Fix IntegrateGQ.sh errors due to presence of variants of just one type #760
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This PR addresses Issue #759.
Description
Brief Description: Addresses an issue in the
IntegrateGQ.shscript where the combination ofset -o pipefail and{ fgrep ... || true; }patterns could cause pipelines to fail prematurely if no matches were found. By removing the curly braces and letting|| trueapply directly tofgrep, the script no longer aborts unexpectedly and continues processing even whenfgrepreturns a non-zero exit code.Testing
IntegrateGq.sh, wherein each variant in its depth & PESR VCFs are of type- note that the run fails.IntegrateGq.sh- note that the run completes successfully.