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enable for bulk too
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Eric Kofman committed Jul 25, 2024
1 parent 2674b1b commit 601b78f
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Showing 5 changed files with 52 additions and 2,525 deletions.
15 changes: 8 additions & 7 deletions marine.py
Original file line number Diff line number Diff line change
Expand Up @@ -330,11 +330,11 @@ def bam_reconfig_launcher(contig):
#total_seconds_for_bams_df.to_csv("{}/bam_reconfiguration_timing.tsv".format(logging_folder), sep='\t')
#pretty_print("Total time to concat and write bams: {} minutes".format(round(total_bam_generation_time/60, 3)))

for c in contigs:
thread = threading.Thread(target=monitor_event, args=(events[c], c, bam_reconfig_launcher))
thread.start()
threads.append(thread)
if barcode_tag:
for c in contigs:
thread = threading.Thread(target=monitor_event, args=(events[c], c, bam_reconfig_launcher))
thread.start()
threads.append(thread)

_, results, total_seconds_for_reads_df, total_reads_processed, counts_summary_df = edit_finder(
bam_filepath,
Expand All @@ -352,8 +352,9 @@ def bam_reconfig_launcher(contig):
)

# Wait for all threads to complete
for thread in threads:
thread.join()
if barcode_tag:
for thread in threads:
thread.join()

total_seconds_for_reads_df.to_csv("{}/edit_finder_timing.tsv".format(logging_folder), sep='\t')

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