diff options
| author | Justin Bedo <cu@cua0.org> | 2018-12-12 10:23:11 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-12-12 10:23:11 +1100 |
| commit | 979bf4c65ad668b668750b58eefa9996f51b1242 (patch) | |
| tree | 64d4064b48e0604185cd1a0ff0c5141c31b1d6a2 /tools/gridss.nix | |
| parent | 10bdecf6c1338d7f531ddf7b41da14dfe4a4ac33 (diff) | |
gridss: refactor identify & annotate variants
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 b85e84e..d47a669 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -15,8 +15,8 @@ rec { collectMetrics = callBionix ./gridss-collectMetrics.nix; extractSVReads = callBionix ./gridss-extractSVReads.nix; assemble = callBionix ./gridss-assemble.nix; - identifyVariants = callBionix ./gridss-identifyVariants.nix; - annotateVariants = callBionix ./gridss-annotateVariants.nix; + identifyVariants = attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify; + annotateVariants = 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); } |