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| author | Justin Bedo <cu@cua0.org> | 2018-10-29 15:32:50 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-10-29 15:32:50 +1100 |
| commit | 8fb986fd88705fc01be7145b04fa229092c1e69e (patch) | |
| tree | 8f5aed2499b7fc6cc1972d7a29f027c760cc1bb0 | |
| parent | 7f11fb044b6e08c53f53a1a0d0d6519fba1ccce3 (diff) | |
bwa-mem: BWA output is query name sorted
| -rw-r--r-- | tools/bwa-mem.nix | 2 |
1 files changed, 1 insertions, 1 deletions
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix index eed488e..3420294 100644 --- a/tools/bwa-mem.nix +++ b/tools/bwa-mem.nix @@ -36,5 +36,5 @@ in stdenv.mkDerivation { ${optionalString bamOutput "| samtools view -b"} \ > $out ''; - passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.none {};}; + passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};}; } |