From 63e1cff1fc8dca9e3c266088c88540b6c8871b30 Mon Sep 17 00:00:00 2001
From: David Lougheed <david.lougheed@gmail.com>
Date: Sat, 3 Feb 2024 23:31:07 -0500
Subject: [PATCH] fix(call): properly wait for realign process to terminate on
 timeout

---
 strkit/call/call_locus.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/strkit/call/call_locus.py b/strkit/call/call_locus.py
index 0cdf605..84dcae9 100644
--- a/strkit/call/call_locus.py
+++ b/strkit/call/call_locus.py
@@ -5,6 +5,8 @@
 import logging
 import multiprocessing as mp
 import multiprocessing.managers as mmg
+import time
+
 import numpy as np
 import pysam
 import operator
@@ -905,7 +907,16 @@ def call_locus(
                 logger_.warning(
                     f"{locus_log_str} - experienced timeout while re-aligning read {rn}. Reverting to BAM alignment.")
                 proc.terminate()
+                time.sleep(0.1)  # wait a little for the process to terminate
             finally:
+                wait_count: int = 0
+                while proc.is_alive():
+                    logger_.warning(f"{locus_log_str} - realign job has still not exited. Waiting 0.5 seconds...")
+                    time.sleep(0.5)
+                    wait_count += 1
+                    if wait_count > 5:
+                        logger_.fatal(f"{locus_log_str} - realign job never exited. Terminating...")
+                        exit(1)
                 proc.close()
 
             if pairs_new is not None: