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Fix infinite loop when contig is shorter than read_len #264

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Merged
joshfactorial merged 1 commit into from
Apr 7, 2026
Merged

Fix infinite loop when contig is shorter than read_len #264

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7 changes: 7 additions & 0 deletions neat/read_simulator/utils/generate_reads.py
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Original file line number Diff line number Diff line change
Expand Up @@ -183,6 +183,13 @@ def generate_reads(
# _LOG.info(f'Sampling reads for thread {thread_index}...')
start_time = time.time()

if len(reference) < options.read_len:
_LOG.warning(
f"Contig '{contig_name}' (length {len(reference)}) is shorter than read_len "
f"({options.read_len}). Skipping contig."
)
return []

# _LOG.debug("Covering dataset.")
t = time.time()
reads = cover_dataset(
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