d4tools 0.3.10 (new formula) (#1858)

Formula/d4tools.rb

@@ -0,0 +1,60 @@
+class D4tools < Formula
+  # cite Hou_2021: "https://doi.org/10.1038/s43588-021-00085-0"
+  desc "Dense Depth Data Dump (D4) Quantitative Data Format"
+  homepage "https://github.com/38/d4-format"
+  url "https://github.com/38/d4-format/archive/refs/tags/v0.3.10.tar.gz"
+  sha256 "d3fbe8f063ed1f89148ae0333abc1d5b955f499fc429254f83af464012678d33"
+  license "MIT"
+  head "https://github.com/38/d4-format.git", branch: "master"
+
+  depends_on "rust" => :build
+  depends_on "rustup"
+
+  def install
+    cd "d4tools" do
+      system "cargo", "install", *std_cargo_args
+    end
+    cd "d4binding" do
+      inreplace "install.sh", "PREFIX=/opt/local", "PREFIX=#{prefix}"
+      system "./install.sh"
+      rm "#{lib}/libd4binding.d"
+    end
+  end
+
+  test do
+    resource "small.bam" do
+      url "https://github.com/38/d4-format/raw/master/d4tools/test/create/from-bam/small.bam"
+      sha256 "1bb389b38901139bacbe70906b833a2e572676cd87783120193dd0902a63c0b1"
+    end
+    resource "small.bam.bai" do
+      url "https://github.com/38/d4-format/raw/master/d4tools/test/create/from-bam/small.bam.bai"
+      sha256 "a01a850ca0b331145f61048293cf71ecb264962348bd8ebfc9a1249eb95a0fa5"
+    end
+    resources.each { |r| r.stage(testpath) }
+    system "#{bin}/d4tools", "create", "--mapping-qual", "0", "small.bam", "small.d4"
+    assert_match "1\t10158\t20000\t0", shell_output("#{bin}/d4tools view small.d4")
+
+    (testpath/"test.c").write <<~EOS
+      #include <stdio.h>
+      #include <d4.h>
+
+      int main(int argc, char** argv)
+      {
+          d4_file_t* fp = d4_open("small.d4", "r");
+
+          d4_file_metadata_t mt = {};
+          d4_file_load_metadata(fp, &mt);
+
+          int i;
+          for(i = 0; i < mt.chrom_count; i++)
+              printf("# %s %d", mt.chrom_name[i], mt.chrom_size[i]);
+
+          d4_close(fp);
+          return 0;
+      }
+    EOS
+    system ENV.cc, "test.c", "-o", "test",
+                    "-ld4binding", "-I#{include}", "-L#{lib}"
+    assert_match "# 1 20000", shell_output("./test")
+  end
+end