From 59edb7d9c37a688c8c408508c1a9ae5d37df348f Mon Sep 17 00:00:00 2001
From: lezhou8 <lezhou@protonmail.com>
Date: Fri, 24 Mar 2023 11:15:50 +1100
Subject: samtools.queryRegion: queries regions from a fasta file

Only the indexing functionality of samtools faidx is used, rather than also the region querying functionality.
---
 tools/samtools-queryRegion.nix | 22 ++++++++++++++++++++++
 tools/samtools.nix             |  1 +
 2 files changed, 23 insertions(+)
 create mode 100644 tools/samtools-queryRegion.nix

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
+  '';
+}
diff --git a/tools/samtools.nix b/tools/samtools.nix
index e0c45dd..32a563c 100644
--- a/tools/samtools.nix
+++ b/tools/samtools.nix
@@ -13,4 +13,5 @@ with bionix;
   markdup = callBionixE ./samtools-markdup.nix;
   fixmate = callBionixE ./samtools-fixmate.nix;
   tabix = callBionixE ./samtools-tabix.nix;
+  queryRegion = callBionixE ./samtools-queryRegion.nix;
 }
-- 
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