New formula: vcftools

Closes Homebrew/homebrew#7920.

Signed-off-by: Jack Nagel <jacknagel@gmail.com>

Formula/vcftools.rb

@@ -0,0 +1,57 @@
+require 'formula'
+
+class Vcftools < Formula
+  url 'http://downloads.sourceforge.net/project/vcftools/vcftools_0.1.7.tar.gz'
+  homepage 'http://vcftools.sourceforge.net/index.html'
+  md5 'd3e68027a7fe40d3f8cb28c3006c7248'
+
+  def install
+    system "make install PREFIX=#{prefix} CPP=#{ENV.cxx}"
+  end
+
+  def test
+    system "vcftools"
+  end
+
+  def caveats; <<-EOS.undent
+    To use the Perl modules, make sure Vcf.pm, VcfStats.pm, and FaSlice.pm
+    are included in your PERL5LIB environment variable:
+      export PERL5LIB=#{HOMEBREW_PREFIX}/lib/perl5/site_perl:${PERL5LIB}
+    EOS
+  end
+
+  def patches
+    # Install Perl modules to /lib/perl5/site_perl and ensure VcfStats.pm is installed
+    # This is fixed in vcf source tree, will not be needed after version 0.1.7
+    DATA
+  end
+end
+
+__END__
+diff --git a/Makefile b/Makefile
+index 39c042b..055afd0 100644
+--- a/Makefile
++++ b/Makefile
+@@ -17,7 +17,7 @@ ifndef PREFIX
+     export PREFIX = $(dir $(realpath $(lastword $(MAKEFILE_LIST))))
+ endif
+ export BINDIR = ${PREFIX}/bin
+-export MODDIR = ${PREFIX}/lib
++export MODDIR = ${PREFIX}/lib/perl5/site_perl
+ 
+ DIRS = cpp perl
+ install:
+
+diff --git a/perl/Makefile b/perl/Makefile
+index 222b75d..2e8b49f 100644
+--- a/perl/Makefile
++++ b/perl/Makefile
+@@ -1,7 +1,7 @@
+ 
+ BIN = vcf-compare fill-aa vcf-annotate vcf-merge vcf-isec vcf-stats vcf-to-tab fill-an-ac \
+     vcf-query vcf-convert vcf-subset vcf-validator vcf-concat vcf-sort
+-MOD = FaSlice.pm Vcf.pm
++MOD = FaSlice.pm Vcf.pm VcfStats.pm
+ 
+ install:
+ 	    @for i in $(BIN); do cp $(CURDIR)/$$i $(BINDIR)/$$i; done; \