aboutsummaryrefslogtreecommitdiff
path: root/examples
diff options
context:
space:
mode:
authorJustin Bedo <cu@cua0.org>2021-07-28 08:07:32 +1000
committerJustin Bedo <cu@cua0.org>2021-07-28 09:17:56 +1000
commited98174bbefc85f9895c870fdb7518e2a534a150 (patch)
tree913c1eb5cb384213d22af6cf4f4e2b8fd2a51276 /examples
parent134f5e0bfcd5f22e3adee4b707e10693cf71e635 (diff)
bugfix: use unsorted type for alignment output
Most aligners are only pseudo-name sorted (i.e., pairs adjacant).
Diffstat (limited to 'examples')
-rw-r--r--examples/call.nix1
-rw-r--r--examples/ex-tnpair/tnpair.nix1
2 files changed, 2 insertions, 0 deletions
diff --git a/examples/call.nix b/examples/call.nix
index 8c4f073..8a38fdb 100644
--- a/examples/call.nix
+++ b/examples/call.nix
@@ -12,6 +12,7 @@ with lib;
let
preprocess = flip pipe [
(bwa.align { inherit ref; })
+ (samtools.sort { nameSort = true; })
(samtools.fixmate {})
(samtools.sort {})
(samtools.markdup {})
diff --git a/examples/ex-tnpair/tnpair.nix b/examples/ex-tnpair/tnpair.nix
index 70f5514..9e6befe 100644
--- a/examples/ex-tnpair/tnpair.nix
+++ b/examples/ex-tnpair/tnpair.nix
@@ -12,6 +12,7 @@ let
preprocess = s: pipe s [
fetch
(align { preset = "sr"; ref = ref.grch38.seq; flags = "-R'@RG\\tID:${s.type}\\tSM:${s.type}'"; })
+ (sort { nameSort = true; })
(fixmate {})
(sort { })
(markdup { })