Fix #213

bcftools.sort is passed tempfile.gettempdir
ACEnglish · May 19, 2024 · 7d8c496 · 7d8c496
1 parent e10cd4d
commit 7d8c496
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/truvari/utils.py b/truvari/utils.py
@@ -431,7 +431,7 @@ def compress_index_vcf(fn, fout=None, remove=True):
         fout = fn + '.gz'
     m_tmp = make_temp_filename(suffix='.vcf')
     with open(m_tmp, 'w') as out_hdlr:
-        out_hdlr.write(bcftools.sort(fn))
+        out_hdlr.write(bcftools.sort(fn, "--temp-dir", tempfile.gettempdir()))
     pysam.tabix_compress(m_tmp, fout, force=True)
     pysam.tabix_index(fout, force=True, preset="vcf")
     if remove: