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| author | l-d-s <distefano.l@wehi.edu.au> | 2018-11-07 16:39:47 +1100 |
|---|---|---|
| committer | l-d-s <distefano.l@wehi.edu.au> | 2018-11-07 16:39:47 +1100 |
| commit | 886af7beaaa98ac32db88a7453d917409cf11ae8 (patch) | |
| tree | 8d947c091f2951d8b6a524f8f690bd1ddc227d54 | |
| parent | c45a6b1c1b68cd08efe55ec1df197c0c26b5ca49 (diff) | |
Fix to gridss.
| -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 d46a8ce..792d279 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -16,6 +16,6 @@ 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); } |