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use system temp files for temporary snf files #463

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use system temp files for temporary snf files #463

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7 changes: 4 additions & 3 deletions src/sniffles/parallel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
from argparse import Namespace
from dataclasses import dataclass
from typing import Optional, Union, Callable
import tempfile

import pysam

Expand Down Expand Up @@ -163,15 +164,15 @@ def execute(self) -> CallResult:
result = CallResult(self, svcalls, read_count)

if config.snf is not None: # and len(svcandidates):
snf_filename = f"{config.snf}.tmp_{self.id}.snf"
fd, snf_filename = tempfile.mkstemp()

with open(snf_filename, "wb") as handle:
with open(fd,"wb") as handle:
snf_out = snf.SNFile(config, handle)
for cand in svcandidates:
snf_out.store(cand)
snf_out.annotate_block_coverages(self.lead_provider)
snf_out.write_and_index()
handle.close()

result.snf_filename = snf_filename
result.snf_index = snf_out.get_index()
result.snf_total_length = snf_out.get_total_length()
Expand Down