1 files changed, 23 insertions, 0 deletions
diff --git a/tools/bwa-index2.nix b/tools/bwa-index2.nix
new file mode 100644
index 0000000..f5cc69b
--- /dev/null
+++ b/tools/bwa-index2.nix
@@ -0,0 +1,23 @@
+{ bionix
+, flags ? null
+}:
+
+ref:
+
+with bionix;
+with lib;
+with types;
+
+assert (matchFiletype "bwa-index" { fa = _: true; } ref);
+
+stage {
+  name = "bwa-index2";
+  buildInputs = with pkgs; [ bionix.bwa.app2 ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    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
+  '';
+}