diff options
| author | Justin Bedo <cu@cua0.org> | 2020-08-10 09:41:10 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2020-08-10 09:41:10 +1000 |
| commit | bae57d22d7a626c12660f966eba0d2514d376860 (patch) | |
| tree | 63c6bc0a681d1ff528d5a066efb78c57986cd1dc /tools | |
| parent | c3af7841394bbba1433a4e7e3e4aa225c697c81d (diff) | |
bwa: alt regex generalisation
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/bwa-index.nix | 4 |
1 files changed, 3 insertions, 1 deletions
diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix index 17b651f..65d9bd5 100644 --- a/tools/bwa-index.nix +++ b/tools/bwa-index.nix @@ -1,5 +1,6 @@ { bionix , flags ? null +, altRegex ? "^>.*_alt$" }: ref: @@ -18,6 +19,7 @@ stage { bwa 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; } |