From 1cde8c9b92b2ce0447985036bc600e84eaaef004 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 3 Feb 2012 07:28:09 +0000
Subject: [PATCH] added FastqIndex to fastq.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1741 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_ruby/lib/maasha/fastq.rb | 60 ++++++++++++++++++++++++++++++++++-
 1 file changed, 59 insertions(+), 1 deletion(-)

diff --git a/code_ruby/lib/maasha/fastq.rb b/code_ruby/lib/maasha/fastq.rb
index e2a96ea..77a4706 100644
--- a/code_ruby/lib/maasha/fastq.rb
+++ b/code_ruby/lib/maasha/fastq.rb
@@ -28,8 +28,9 @@ require 'maasha/filesys'
 # Error class for all exceptions to do with FASTQ.
 class FastqError < StandardError; end
 
+# Class for parsing FASTQ entries from an ios and return as Seq objects.
 class Fastq < Filesys
-  # Method to get the next FASTQ entry form an ios and return this
+  # Method to get the next FASTQ entry from an ios and return this
   # as a Seq object. If no entry is found or eof then nil is returned.
   def get_entry
     begin
@@ -51,5 +52,62 @@ class Fastq < Filesys
   end
 end
 
+# Class for indesing FASTQ entries. The index will be
+# a hash with the FASTQ sequence name as key and a 
+# FastqElem as value. The latter contains info on
+# byte offset and length for each entry.
+class FastqIndex
+  HEADCHAR = 1
+  NEWLINE  = 1
+
+  attr_accessor :ios
+
+  # Method to initialize a FastqIndex object. For reading
+  # entries from file an _ios_ object must be supplied.
+  def initialize(ios)
+    @ios    = ios
+    @index  = {}
+    @offset = 0
+  end
+
+  # Method to add a Fastq entry to a FastqIndex.
+  def add(entry)
+    offset_seq  = @offset + HEADCHAR + entry.seq_name.length + NEWLINE
+    offset_qual = @offset + HEADCHAR + entry.seq_name.length + NEWLINE + entry.length + NEWLINE + HEADCHAR + NEWLINE
+
+    @index[entry.seq_name] = FastqElem.new(offset_seq, offset_qual, entry.length)
+    
+    @offset += HEADCHAR + entry.seq_name.length + NEWLINE + entry.length + NEWLINE + HEADCHAR + NEWLINE + entry.length + NEWLINE
+  end
+
+  # Method to read from file a Fastq entry from an indexed position,
+  # and return the entry as a Seq object.
+  def get(seq_name)
+    raise FastqError, "Sequence name: #{seq_name} not found in index." unless @index.has_key? seq_name
+
+    elem = @index[seq_name]
+    @ios.sysseek(elem.offset_seq)
+    seq = @ios.sysread(elem.length)
+    @ios.sysseek(elem.offset_qual)
+    qual = @ios.sysread(elem.length)
+
+    Seq.new(seq_name, seq, nil, qual)
+  end
+
+  private
+
+  # Class for storing index information to be used
+  # with disk based index.
+  class FastqElem
+    attr_reader :offset_seq, :offset_qual, :length
+
+    def initialize(offset_seq, offset_qual, length)
+      @offset_seq  = offset_seq
+      @offset_qual = offset_qual
+      @length      = length
+    end
+  end
+end
+
 
 __END__
-- 
2.39.2