From 64f8b0cb124445620b30e10e268fd7670ccb3189 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 19 Feb 2021 11:18:10 +1100
Subject: samtools-index: support cram indexing

---
 test-tnpair.nix          |  1 +
 tools/samtools-index.nix | 11 +++++++----
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/test-tnpair.nix b/test-tnpair.nix
index 70fb5c8..7cc5453 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -64,6 +64,7 @@ let
   };
 
   testNaming = linkOutputs {
+    crai = samtools.index {} (samtools.view { outfmt = types.toCram; } tnpairResult.alignments.tumour);
     kallisto = kallisto.quant {inherit ref;} (attrValues tnpair.tumour.files);
     facets = facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];};
     cnvkit = cnvkitResults.cnvs;
diff --git a/tools/samtools-index.nix b/tools/samtools-index.nix
index d0f8d7a..62ee4c9 100644
--- a/tools/samtools-index.nix
+++ b/tools/samtools-index.nix
@@ -8,16 +8,19 @@ with bionix;
 with lib;
 with types;
 
-assert (matchFiletype "samtools-index" { bam = _: true; } input);
+assert (matchFiletype "samtools-index" { bam = _: true; cram = _: true; } input);
 assert (matchFileSorting "samtools-index" { coord = _: true; } input);
 
+let
+  ext = matchFiletype "samtools-index-ext" { bam = _: "bam"; cram = _: "cram"; };
+in
+
 stage {
   name = "samtools-index";
   buildInputs = with pkgs; [ samtools ];
   buildCommand = ''
-    ln -s ${input} input.bam
-    samtools index -@ $NIX_BUILD_CORES ${optionalString (flags != null) flags} input.bam
-    cp input.bam.bai $out
+    ln -s ${input} input.${ext input}
+    samtools index -@ $NIX_BUILD_CORES ${optionalString (flags != null) flags} input.${ext input} $out
   '';
   passthru.multicore = true;
 }
-- 
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