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fix(call): properly terminate realign process if it times out
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davidlougheed committed Feb 3, 2024
1 parent 9fd40cb commit 6b267e1
Showing 1 changed file with 1 addition and 0 deletions.
1 change: 1 addition & 0 deletions strkit/call/call_locus.py
Original file line number Diff line number Diff line change
Expand Up @@ -904,6 +904,7 @@ def call_locus(
except queue.Empty:
logger_.warning(
f"{locus_log_str} - experienced timeout while re-aligning read {rn}. Reverting to BAM alignment.")
proc.terminate()
finally:
proc.close()

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