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authorJustin Bedo <cu@cua0.org>2022-01-25 12:04:05 +1100
committerJustin Bedo <cu@cua0.org>2022-01-25 12:04:05 +1100
commit5fc4c8fc0ce707c57204e57a2cd058c019bc8bd8 (patch)
tree9943a6526ff28b2af832d7e30852d2840219ef96 /tools
parent173e7a758569796a91120379853b94f35dcc4a81 (diff)
add tabix indexing
Diffstat (limited to 'tools')
-rw-r--r--tools/samtools-tabix.nix22
-rw-r--r--tools/samtools.nix1
2 files changed, 23 insertions, 0 deletions
diff --git a/tools/samtools-tabix.nix b/tools/samtools-tabix.nix
new file mode 100644
index 0000000..a493b9d
--- /dev/null
+++ b/tools/samtools-tabix.nix
@@ -0,0 +1,22 @@
+{ bionix
+, flags ? null
+}:
+
+input:
+
+with bionix;
+with lib;
+with types;
+
+assert (matchFiletype "samtools-tabix" { bgz = _: true; } input);
+
+stage {
+
+ name = "samtools-tabix";
+ buildInputs = with pkgs; [ htslib ];
+ buildCommand = ''
+ ln -s ${input} input.bgz
+ tabix input.bgz
+ cp input.bgz.tbi $out
+ '';
+}
diff --git a/tools/samtools.nix b/tools/samtools.nix
index 27f3f73..e0c45dd 100644
--- a/tools/samtools.nix
+++ b/tools/samtools.nix
@@ -12,4 +12,5 @@ with bionix;
merge = callBionixE ./samtools-merge.nix;
markdup = callBionixE ./samtools-markdup.nix;
fixmate = callBionixE ./samtools-fixmate.nix;
+ tabix = callBionixE ./samtools-tabix.nix;
}