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-rw-r--r--tools/gridss.nix11
1 files changed, 9 insertions, 2 deletions
diff --git a/tools/gridss.nix b/tools/gridss.nix
index 009752e..5bb9484 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -17,6 +17,13 @@ rec {
assemble = callBionixE ./gridss-assemble.nix;
identifyVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify);
annotateVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate);
- preprocessBam = input: with samtools; sort {} (gridss.softClipsToSplitReads {} (gridss.computeSamTags {} (sort {nameSort = true;} (gridss.extractSVReads {} (markdup {} (sort {} (fixmate {mateScore = true;} (sort {nameSort = true;} input))))))));
- call = inputs: bionix.gridss.annotateVariants {} (map gridss.preprocessBam inputs);
+ preprocessBam = with samtools;
+ pipe [
+ (gridss.extractSVReads {})
+ (sort {nameSort = true;})
+ (gridss.computeSamTags {})
+ (gridss.softClipsToSplitReads {})
+ (sort {})
+ ];
+ call = inputs: gridss.annotateVariants {} (map gridss.preprocessBam inputs);
}