The bcftools head command does not support -o either

pysam-developers · Oct 22, 2024 · 256adfc · 256adfc
1 parent a25bd31
commit 256adfc
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/pysam/libcutils.pyx b/pysam/libcutils.pyx
@@ -345,7 +345,7 @@ def _pysam_dispatch(collection,
         if collection == "bcftools":
             # in bcftools, most methods accept -o, the exceptions
             # are below:
-            if method not in ("index", "roh", "stats"):
+            if method not in ("head", "index", "roh", "stats"):
                 stdout_option = "-o {}"
         elif method in MAP_STDOUT_OPTIONS[collection]:
             # special case - samtools view -c outputs on stdout