1 files changed, 22 insertions, 0 deletions
diff --git a/tools/samtools-queryRegion.nix b/tools/samtools-queryRegion.nix
new file mode 100644
index 0000000..650e4f4
--- /dev/null
+++ b/tools/samtools-queryRegion.nix
@@ -0,0 +1,22 @@
+{ bionix
+, flags ? null
+, regions ? []
+}:
+
+input:
+
+with bionix;
+with lib;
+with types;
+
+assert (matchFiletype "samtools-queryRegion" { fa = _: true; } input);
+
+stage {
+
+  name = "samtools-faidx";
+  buildInputs = with pkgs; [ samtools ];
+  buildCommand = ''
+    ln -s ${input} input.fasta
+    samtools faidx ${optionalString (flags != null) flags} input.fasta ${concatStringsSep " " regions} > $out
+  '';
+}