rammap 1.1.2 (new formula)

Formula/r/rammap.rb

@@ -0,0 +1,42 @@
+class Rammap < Formula
+  desc "Extensible and performant aligner and read mapper"
+  homepage "https://github.com/jwanglab/rammap"
+  url "https://github.com/jwanglab/rammap/archive/refs/tags/v1.1.2.tar.gz"
+  sha256 "d6d349495da8fb26e50ce6408235a587a297f666063f01ca8ebf05439b47d33c"
+  license "MIT"
+  head "https://github.com/jwanglab/rammap.git", branch: "main"
+
+  depends_on "rust" => :build
+
+  def install
+    system "cargo", "install", *std_cargo_args(path: "rammap")
+  end
+
+  test do
+    # Deterministic pseudo-random reference; a repetitive one would not seed.
+    seed = 12_345
+    reference = Array.new(1200) do
+      seed = ((seed * 1_103_515_245) + 12_345) % (2**31)
+      "ACGT"[(seed >> 16) % 4]
+    end.join
+    (testpath/"ref.fa").write ">chr1\n#{reference.scan(/.{1,60}/).join("\n")}\n"
+
+    # A read lifted verbatim out of the reference, so it must align exactly.
+    read = reference[300, 200]
+    (testpath/"reads.fq").write "@read1\n#{read}\n+\n#{"I" * read.length}\n"
+
+    paf = shell_output("#{bin}/rammap -x map-ont ref.fa reads.fq 2>/dev/null")
+    fields = paf.lines.first.chomp.split("\t")
+    assert_equal "read1", fields[0]
+    assert_equal "+", fields[4]
+    assert_equal "chr1", fields[5]
+    assert_equal "1200", fields[6]
+    assert_equal "60", fields[11]
+    assert_operator fields[9].to_i, :>=, 190
+
+    sam = shell_output("#{bin}/rammap -x map-ont -a ref.fa reads.fq 2>/dev/null")
+    assert_match "@SQ\tSN:chr1\tLN:1200", sam
+    assert_match "200M", sam
+    assert_match "NM:i:0", sam
+  end
+end