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| author | Justin Bedo <cu@cua0.org> | 2018-11-15 15:13:50 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-11-15 15:13:50 +1100 |
| commit | c2da3532235bd45ddb1105600d4ba74a70dadeca (patch) | |
| tree | 58d28cb7738d063e4df8416b4cff5fd3ab37f77a | |
| parent | 08f9d475e616c1034bcb04b8ad9ac4f139b4be9e (diff) | |
gridss.softClipsToSplitReads: sort ordering is not preserved
NB: this breaks gridss.preprocessBam
| -rw-r--r-- | tools/gridss-softClipsToSplitReads.nix | 6 |
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 {}; } } |