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authorl-d-s <distefano.l@wehi.edu.au>2018-11-07 16:39:47 +1100
committerl-d-s <distefano.l@wehi.edu.au>2018-11-07 16:39:47 +1100
commit886af7beaaa98ac32db88a7453d917409cf11ae8 (patch)
tree8d947c091f2951d8b6a524f8f690bd1ddc227d54
parentc45a6b1c1b68cd08efe55ec1df197c0c26b5ca49 (diff)
Fix to gridss.
-rw-r--r--tools/gridss.nix4
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);
}