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| author | Justin Bedo <cu@cua0.org> | 2020-08-10 09:38:03 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2020-08-10 09:38:03 +1000 |
| commit | c3af7841394bbba1433a4e7e3e4aa225c697c81d (patch) | |
| tree | 6f10b85b213619d714577c9ba00995b0ba6d752e /tools/bwa-index2.nix | |
| parent | c6b5b6dd77715c53acb0a19a7216e6d2cdb8dd91 (diff) | |
bwa2: update to release
Diffstat (limited to 'tools/bwa-index2.nix')
| -rw-r--r-- | tools/bwa-index2.nix | 4 |
1 files changed, 3 insertions, 1 deletions
diff --git a/tools/bwa-index2.nix b/tools/bwa-index2.nix index f5cc69b..b02d007 100644 --- a/tools/bwa-index2.nix +++ b/tools/bwa-index2.nix @@ -1,5 +1,6 @@ { bionix , flags ? null +, altRegex ? "^>.*_alt$" }: ref: @@ -18,6 +19,7 @@ stage { bwa-mem2 index ${optionalString (flags != null) flags} ref.fa mkdir $out mv ref.fa.* $out - grep '^>[^ \t]*_alt$' ref.fa | tr -d '^>' > $out/idxbase.alt || true + grep -P '${altRegex}' ref.fa | tr -d '^>' > $out/idxbase.alt || true ''; + stripStorePaths = false; } |