bugfix: use unsorted type for alignment output

Most aligners are only pseudo-name sorted (i.e., pairs adjacant).

1 files changed, 1 insertions, 1 deletions

diff --git a/tools/bwa-mem2.nix b/tools/bwa-mem2.nix
index 3de1944..b16b7ea 100644
--- a/tools/bwa-mem2.nix
+++ b/tools/bwa-mem2.nix
@@ -35,6 +35,6 @@ in stage {
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
   passthru.multicore = true;
 }