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| author | l-d-s <l@sdf.org> | 2018-11-15 16:11:14 +1100 |
|---|---|---|
| committer | l-d-s <l@sdf.org> | 2018-11-15 16:11:14 +1100 |
| commit | 5ad075658eea3d783bac013aae476dd22a371e71 (patch) | |
| tree | d0b38bcdb4e3aeaabbcd99aee24bb8a40ea86f24 /tools/gridss.nix | |
| parent | dfb20e1741e8785fae8527c881954de33b7c72ac (diff) | |
| parent | c2da3532235bd45ddb1105600d4ba74a70dadeca (diff) | |
Merge branch 'master' of https://github.com/PapenfussLab/bionix
Diffstat (limited to 'tools/gridss.nix')
| -rw-r--r-- | tools/gridss.nix | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/tools/gridss.nix b/tools/gridss.nix index bc2f0b8..1e4e2d1 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -17,6 +17,6 @@ rec { assemble = callBionix ./gridss-assemble.nix; identifyVariants = callBionix ./gridss-identifyVariants.nix; annotateVariants = callBionix ./gridss-annotateVariants.nix; - preprocessBam = input: with samtools; markdup {} (sort {} (fixmate {mateScore = true;} (softClipsToSplitReads {} (computeSamTags {} (sort {nameSort = true;} input))))); - call = inputs: annotateVariants {} (map preprocessBam inputs); + preprocessBam = input: with samtools; markdup {} (sort {} (fixmate {mateScore = true;} (bionix.gridss.softClipsToSplitReads {} (bionix.gridss.computeSamTags {} (sort {nameSort = true;} input))))); + call = inputs: bionix.gridss.annotateVariants {} (map bionix.gridss.preprocessBam inputs); } |