From 9a70a25d6b7771df7ca53fcc34d61f582296e384 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 10 Jan 2019 12:20:51 +1100
Subject: facets: init

---
 tools/facets-call.nix | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 tools/facets-call.nix

(limited to 'tools/facets-call.nix')

diff --git a/tools/facets-call.nix b/tools/facets-call.nix
new file mode 100644
index 0000000..021cacc
--- /dev/null
+++ b/tools/facets-call.nix
@@ -0,0 +1,24 @@
+{bionix}:
+
+{vcf, bams}:
+
+with bionix;
+with types;
+with lib;
+
+assert (matchFiletype "facets-call-vcf" { vcf = _: true; } vcf);
+assert (all (matchFiletype "facets-call-bam" { bam = _: true; }) bams);
+assert (all (matchFileSorting "facets-call-bam" { coord = _: true; }) bams);
+
+stage {
+  name = "facets";
+  buildInputs = [ facets.app ];
+  buildCommand = ''
+    # Facets requires lexical sorting on the VCF files
+    grep '^#' ${vcf} > input.vcf
+    grep -v '^#' ${vcf} | LC_ALL=C sort -t $'\t' -k1,1 -k2,2n >> input.vcf || true
+
+    # Now actually run facets
+    snp-pileup input.vcf $out ${concatStringsSep " " bams}
+  '';
+}
-- 
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