From 256adfc55b4ab6d2b3a473a2548d3cd7bca60ffc Mon Sep 17 00:00:00 2001 From: John Marshall Date: Tue, 22 Oct 2024 22:25:07 +1300 Subject: [PATCH] The `bcftools head` command does not support -o either --- pysam/libcutils.pyx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pysam/libcutils.pyx b/pysam/libcutils.pyx index cfdcc1f2..72eaee55 100644 --- 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