diff options
| author | Justin Bedo <cu@cua0.org> | 2021-07-28 08:07:32 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2021-07-28 09:17:56 +1000 |
| commit | ed98174bbefc85f9895c870fdb7518e2a534a150 (patch) | |
| tree | 913c1eb5cb384213d22af6cf4f4e2b8fd2a51276 /examples | |
| parent | 134f5e0bfcd5f22e3adee4b707e10693cf71e635 (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.nix | 1 | ||||
| -rw-r--r-- | examples/ex-tnpair/tnpair.nix | 1 |
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 { }) |