diff options
| author | Justin Bedo <cu@cua0.org> | 2018-12-11 14:11:21 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-12-11 14:11:21 +1100 |
| commit | d79fc6785f2b8714fa2762bd07a9a9f937bf4513 (patch) | |
| tree | c9ff02450c40bd27d4a424e572f2928ac5c2ccc7 | |
| parent | 2a8c14c6fabc914b8cc173313a685f2b94a26aea (diff) | |
gridss: fix softClipsToSplitReads after assembly
| -rw-r--r-- | tools/gridss-annotateVariants.nix | 4 | ||||
| -rw-r--r-- | tools/gridss-assemble.nix | 2 | ||||
| -rw-r--r-- | tools/gridss-softClipsToSplitReads.nix | 2 |
3 files changed, 4 insertions, 4 deletions
diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix index 655b268..3560f77 100644 --- a/tools/gridss-annotateVariants.nix +++ b/tools/gridss-annotateVariants.nix @@ -5,7 +5,7 @@ , indexAttrs ? {} , assemblyAttrs ? {} , collectMetricsAttrs ? {} -, softClipsToSplitReadsAttrs ? {} +, softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; } , identifyVariantsAttrs ? {} , flags ? null , config ? null @@ -45,7 +45,7 @@ let ln -s ${bionix.samtools.index indexAttrs input} $WRKDIR/$BASENAME.sv.bai ''; - assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.samtools.sort { nameSort = true;} (bionix.gridss.assemble assemblyAttrs inputs))); + assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.gridss.assemble assemblyAttrs inputs)); in assert (all sorted inputs); diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix index 847830a..a8124e0 100644 --- a/tools/gridss-assemble.nix +++ b/tools/gridss-assemble.nix @@ -55,5 +55,5 @@ stdenv.mkDerivation rec { WORKING_DIR=$TMPDIR/ \ TMP_DIR=$TMPDIR/ ''; - passthru.filetype = filetype.bam { ref = ref; sorting = sort.coord {}; }; + passthru.filetype = filetype.bam { ref = ref; sorting = sort.name {}; }; } diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index 9bce063..c23168f 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -35,5 +35,5 @@ stdenv.mkDerivation rec { ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ WORKER_THREADS=$NIX_BUILD_CORES ''; - passthru.filetype = filetype.bam { ref = ref; sorting = matchFileSorting "grids-softClipsToSplitReads" { coord = _: input.sorting; name = _: sort.none {}; none = _: input.sorting;} input;}; + passthru.filetype = filetype.bam { ref = ref; sorting = sort.none {}; }; } |