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authorJustin Bedo <cu@cua0.org>2018-11-15 15:13:50 +1100
committerJustin Bedo <cu@cua0.org>2018-11-15 15:13:50 +1100
commitc2da3532235bd45ddb1105600d4ba74a70dadeca (patch)
tree58d28cb7738d063e4df8416b4cff5fd3ab37f77a
parent08f9d475e616c1034bcb04b8ad9ac4f139b4be9e (diff)
gridss.softClipsToSplitReads: sort ordering is not preserved
NB: this breaks gridss.preprocessBam
-rw-r--r--tools/gridss-softClipsToSplitReads.nix6
1 files changed, 1 insertions, 5 deletions
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index b35d41d..5fce894 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -37,9 +37,5 @@ stdenv.mkDerivation rec {
${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
WORKER_THREADS=$NIX_BUILD_CORES
'';
- passthru.filetype =
- if alignerStreaming then
- filetype.bam { ref = ref; sort = sorting.none {}; }
- else
- input.filetype;
+ passthru.filetype = filetype.bam { ref = ref; sort = sorting.none {}; }
}