Fix IntegrateGQ.sh errors due to presence of variants of just one type #760
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This PR addresses Issue #759.
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 leveragingawkwithARGIND, the script no longer fails silently and continues processing regardless of theSVTYPEmakeup of the shard.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.