From 8c29f7d34fd713d7630ef081fd8cefbb83ef201b Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 7 Oct 2022 15:51:34 +1100
Subject: add ex4

---
 day2/ex4-bwa/solution.nix | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 day2/ex4-bwa/solution.nix

(limited to 'day2/ex4-bwa/solution.nix')

diff --git a/day2/ex4-bwa/solution.nix b/day2/ex4-bwa/solution.nix
new file mode 100644
index 0000000..79fc7dc
--- /dev/null
+++ b/day2/ex4-bwa/solution.nix
@@ -0,0 +1,19 @@
+{bionix}:
+with bionix; let
+  input = {
+    input1 = fetchFastQ {
+      url = "https://raw.githubusercontent.com/PapenfussLab/bionix/master/examples/sample1-1.fq";
+      sha256 = "sha256-qE6s8hKowiz3mvCq8/7xAzUz77xG9rAcsI2E50xMAk4=";
+    };
+    input2 = fetchFastQ {
+      url = "https://raw.githubusercontent.com/PapenfussLab/bionix/master/examples/sample1-2.fq";
+      sha256 = "sha256-s02R49HX/qeJp4t/eZwsKwV9D07uLGId8CEpU2dB8zM=";
+    };
+  };
+
+  ref = fetchFastA {
+    url = "https://raw.githubusercontent.com/PapenfussLab/bionix/master/examples/ref.fa";
+    sha256 = "sha256-V3zqOJFuGtukDRQttK/pGfKofgOlKrridHaWYhGGyWs=";
+  };
+in
+  samtools.sort {} (bwa.align {inherit ref;} input)
-- 
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