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-rw-r--r--tools/gridss-annotateVariants.nix4
-rw-r--r--tools/gridss-assemble.nix2
-rw-r--r--tools/gridss-softClipsToSplitReads.nix2
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 {}; };
}