added ruby version of read_sam

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1613 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/read_sam b/bp_bin/read_sam
new file mode 100755 (executable)
index 0000000..69cbf64
--- /dev/null
+++ b/bp_bin/read_sam
@@ -0,0 +1,71 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This program is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read SAM entries from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/biopieces'
+require 'maasha/sam'
+
+casts = []
+casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'num',     :short=>'n', :type=>'uint',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+num  = 0
+last = false
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    output.puts record
+  end
+
+  if options.has_key? :data_in
+    options[:data_in].each do |file|
+      Sam.open(file, mode='r') do |sam|
+        sam.each do |entry|
+          output.puts Sam.to_bp(entry)
+          num += 1
+
+          if options.has_key? :num and options[:num] == num
+            last = true
+            break
+          end
+        end
+      end
+
+      break if last
+    end
+  end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__