bio-pileup_iterator 0.0.1

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem 'bio', '>=1.4.2'
+gem 'bio-samtools', '>=0.5.3'
+gem 'bio-logger', '>=1.0.0'
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "bundler", ">= 1.0.0"
+  gem "jeweler", "~> 1.8.3"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

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+Copyright (c) 2012 Ben J. Woodcroft
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= bio-pileup_iterator
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-pileup_iterator
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-pileup_iterator
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/wwood/bioruby-pileup_iterator
+
+== Cite
+
+  If you use this software, please cite http://dx.doi.org/10.1093/bioinformatics/btq475
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-pileup_iterator
+
+== Copyright
+
+Copyright (c) 2012 Ben J. Woodcroft. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-pileup_iterator"
+  gem.homepage = "http://github.com/wwood/bioruby-pileup_iterator"
+  gem.license = "MIT"
+  gem.summary = %Q{Iterate through a samtools pileup file}
+  gem.description = %Q{Iterate through a samtools pileup file}
+  gem.email = "donttrustben near gmail.com"
+  gem.authors = ["Ben J. Woodcroft"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-pileup_iterator #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/lib/bio-pileup_iterator.rb

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+require 'bio'
+require 'bio-samtools'
+require 'bio-logger'
+Bio::Log::LoggerPlus.new('bio-pileup_iterator')
+
+require 'bio/db/pileup_iterator'

data/lib/bio/db/pileup_iterator.rb

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+
+
+class Bio::DB::Pileup
+  # Bio::DB::PileupIterator::PileupRead objects that occur at this position
+  attr_accessor :reads
+  
+  def num_deletions
+    return read_bases.gsub(/[^\*]/,'').length
+  end
+end
+
+class Bio::DB::PileupIterator
+  include Enumerable
+  
+  def initialize(io)
+    @io = io
+  end
+
+  # Iterates through the positions of the a pileup, returning an instance of Bio::DB::Pileup complete with an instance variable @reads, an Array of Bio::DB::PileupRead objects.
+  #
+  # Known problems:
+  # * Doesn't record start or ends of each read
+  # * Doesn't lookahead to determine the sequence of each read (though it does give the preceding bases)
+  # * Gives no information with mismatches
+  def each
+    current_ordered_reads = []
+    log = Bio::Log::LoggerPlus['bio-pileup_iterator']
+    
+    @io.each_line do |line|
+      #log.debug "new current_line: #{line.inspect}"
+      pileup = Bio::DB::Pileup.new(line.strip)
+      current_read_index = 0
+      reads_ending = []
+
+      bases = pileup.read_bases
+      #log.debug "new column's read_bases: #{bases.inspect}"
+      #log.debug "pileup entry parsed: #{pileup.inspect}"
+      while bases.length > 0
+        #log.debug "bases remaining: #{bases}    ------------------------"
+        
+        # Firstly, what is the current read we are working with
+        current_read = current_ordered_reads[current_read_index]
+        # if adding a new read
+        if current_read.nil?
+          #log.debug 'adding a new read'
+          current_read = PileupRead.new
+          current_ordered_reads.push current_read
+        else
+          #log.debug 'reusing a read'
+        end
+        matches = nil
+
+        # Now, parse what the current read is
+        if matches = bases.match(/^([ACGTNacgtn\.\,])([\+\-])([0-9]+)([ACGTNacgtn]+)(\${0,1})/)
+          #log.debug "matched #{matches.to_s} as insertion/deletion"
+          
+          # match again to better match the number of inserted bases
+          num_inserted = matches[3].to_i
+          matches = bases.match(/^([ACGTNacgtn\.\,])([\+\-])([0-9]+)([ACGTNacgtn]{#{num_inserted}})(\${0,1})/)
+          raise unless matches
+          
+          # insertion / deletion
+          if matches[1] == '.'
+            raise if !current_read.direction.nil? and current_read.direction != PileupRead::FORWARD_DIRECTION
+            current_read.direction = PileupRead::FORWARD_DIRECTION
+            current_read.sequence = "#{current_read.sequence}#{pileup.ref_base}"
+          elsif matches[1] == ','
+            raise if !current_read.direction.nil? and current_read.direction != PileupRead::REVERSE_DIRECTION
+            current_read.direction = PileupRead::REVERSE_DIRECTION
+            current_read.sequence = "#{current_read.sequence}#{pileup.ref_base}"
+          else
+            # Could sanity check the direction here by detecting case, but eh
+            current_read.sequence = "#{current_read.sequence}#{matches[1]}"
+          end
+          
+          # record the insertion
+          if matches[2] == '+'
+            current_read.add_insertion pileup.pos, matches[3], matches[4]
+          end
+          
+          if matches[5].length > 0
+            #log.debug "Ending this read"
+            # end this read
+            reads_ending.push current_read_index
+          end
+        # currently I don't care about indels, except for the direction, so I'll leave it at that for now
+
+        # end of the read
+        elsif matches = bases.match(/^([\.\,])\$/)
+          #log.debug "matched #{matches.to_s} as end of read"
+          # regular match in some direction, end of read
+          if matches[1]=='.' # if forwards
+            raise if current_read.direction and current_read.direction != PileupRead::FORWARD_DIRECTION
+            current_read.direction = PileupRead::FORWARD_DIRECTION
+            current_read.sequence = "#{current_read.sequence}#{pileup.ref_base}"
+          else # else must be backwards, since it can only be , or .
+            raise if current_read.direction and current_read.direction != PileupRead::REVERSE_DIRECTION
+            current_read.direction = PileupRead::REVERSE_DIRECTION
+            current_read.sequence = "#{current_read.sequence}#{pileup.ref_base}"
+          end
+          #log.debug "current read after deletion: #{current_read.inspect}"
+          reads_ending.push current_read_index
+          
+        # regular match continuuing onwards
+        elsif matches = bases.match(/^\./)
+          #log.debug "matched #{matches.to_s} as forward regular match"
+          # regular match in the forward direction
+          raise if !current_read.direction.nil? and current_read.direction != PileupRead::FORWARD_DIRECTION
+          current_read.direction = PileupRead::FORWARD_DIRECTION
+          #log.debug "before adding this base, current sequence is '#{current_read.sequence}'"
+          current_read.sequence = "#{current_read.sequence}#{pileup.ref_base}"
+          #log.debug "after adding this base, current sequence is '#{current_read.sequence}', ref_base: #{pileup.ref_base}"
+        elsif matches = bases.match(/^\,/)
+          #log.debug "matched #{matches.to_s} as reverse regular match"
+          # regular match in the reverse direction
+          if !current_read.direction.nil? and current_read.direction != PileupRead::REVERSE_DIRECTION
+            error_msg = "Unexpectedly found read a #{current_read.direction} direction read when expecting a positive direction one. This suggests there is a problem with either the pileup file or this pileup parser. Current pileup column #{pileup.inspect}, read #{current_read.inspect}, chomped until #{bases}"
+            log.error error_msg
+            raise Exception, error_msg
+          end
+          current_read.direction = PileupRead::REVERSE_DIRECTION
+          current_read.sequence = "#{current_read.sequence}#{pileup.ref_base}"
+        
+        # starting a new read (possibly with a gap), with an accompanying insertion/deletion
+        elsif matches = bases.match(/^\^.([ACGTNacgtn\.\,\*])([\+\-])([0-9]+)([ACGTNacgtn]+)(\${0,1})/)
+          if matches[1] == '.'
+            #log.debug 'forward match starting a read'
+            current_read.direction = PileupRead::FORWARD_DIRECTION
+            current_read.sequence = "#{current_read.sequence}#{pileup.ref_base}"
+          elsif matches[1] == ','
+            #log.debug 'reverse match starting a read'
+            current_read.direction = PileupRead::REVERSE_DIRECTION
+            current_read.sequence = "#{current_read.sequence}#{pileup.ref_base}"
+          elsif matches[1] == '*'
+            #log.debug 'starting a read with a gap'
+            # leave direction unknown at this point
+            current_read.sequence = "#{current_read.sequence}#{matches[1]}"
+          elsif matches[1] == matches[1].upcase
+            #log.debug 'forward match starting a read, warning of insertion next'
+            current_read.direction = PileupRead::FORWARD_DIRECTION
+            current_read.sequence = "#{current_read.sequence}#{matches[1]}"
+          else
+            #log.debug 'forward match starting a read, warning of insertion next'
+            current_read.direction = PileupRead::REVERSE_DIRECTION
+            current_read.sequence = "#{current_read.sequence}#{matches[1]}"
+          end
+          
+          # record the insertion
+          if matches[2] == '+'
+            current_read.add_insertion pileup.pos, matches[3], matches[4]
+          end
+          
+          if matches[5].length > 0
+            #log.debug "Ending this read"
+            # end this read
+            reads_ending.push current_read_index
+          end
+
+          
+        # regular match, starting a new read
+        elsif matches = bases.match(/^\^.([ACGTNacgtn\.\,\*])(\${0,1})/)
+          if matches[1] == '.'
+            #log.debug 'forward match starting a read'
+            current_read.direction = PileupRead::FORWARD_DIRECTION
+            current_read.sequence = "#{current_read.sequence}#{pileup.ref_base}"
+          elsif matches[1] == ','
+            #log.debug 'reverse match starting a read'
+            current_read.direction = PileupRead::REVERSE_DIRECTION
+            current_read.sequence = "#{current_read.sequence}#{pileup.ref_base}"
+          elsif matches[1] == '*'
+            #log.debug 'gap starting a read'
+            current_read.sequence = "#{current_read.sequence}#{matches[1]}"
+          elsif matches[1] == matches[1].upcase
+            #log.debug 'forward match starting a read, warning of insertion next'
+            current_read.direction = PileupRead::FORWARD_DIRECTION
+            current_read.sequence = "#{current_read.sequence}#{matches[1]}"
+          else
+            #log.debug 'forward match starting a read, warning of insertion next'
+            current_read.direction = PileupRead::REVERSE_DIRECTION
+            current_read.sequence = "#{current_read.sequence}#{matches[1]}"
+          end
+          if matches[2].length > 0
+            #log.debug "Ending this read, even though it started here too.. it happens.."
+            # end this read
+            reads_ending.push current_read_index
+          end
+
+          
+        elsif matches = bases.match(/^\*([\+\-])([0-9]+)([ACGTNacgtn=]+)(\${0,1})/)
+          #log.debug 'gap then insert/delete found'
+          # gap - should already be known from the last position
+          current_read.sequence = "#{current_read.sequence}*"
+          if matches[4].length > 0
+            #log.debug "Ending this read"
+            # end this read
+            reads_ending.push current_read_index
+          end
+                    
+          # record the insertion
+          if matches[1] == '+'
+            current_read.add_insertion pileup.pos, matches[2], matches[3]
+          end
+
+        elsif matches = bases.match(/(^[ACGTNacgtn\*])(\${0,1})/)
+          #log.debug 'mismatch found (or deletion)'
+          # simple mismatch
+          current_read.sequence = "#{current_read.sequence}#{matches[1]}"
+          if matches[2].length > 0
+            #log.debug "Ending this read"
+            reads_ending.push current_read_index
+          end
+        end
+        #log.debug "current read's sequence: #{current_read.sequence}"
+        
+        #raise Exception, "implement mismatch parsing here!!!"
+        raise Exception, "Unexpected Pileup format bases, starting here: #{bases}, from #{pileup.inspect}" if matches.nil?
+        
+        #remove the matched part from the base string for next time
+        bases = bases[matches.to_s.length..bases.length-1]
+
+        current_read_index += 1
+      end
+
+      # Create a new copy of the array and yield that, otherwise when things get deleted they get removed from the yielded array as well (which is unwanted)
+      yielded_array = Array.new(current_ordered_reads)
+      pileup.reads = yielded_array
+      #log.debug "Number of reads yielded: #{pileup.reads.length}"
+      yield pileup
+      
+      # Remove reads that ended. In reverse order since removing the last ones first doesn't mess with the indices beforehand in the array
+      reads_ending.reverse.each do |i|
+        #log.debug "Deleting read of index #{i} (total reads #{current_ordered_reads.length}): #{current_ordered_reads[i].inspect}"
+        current_ordered_reads.delete_at i
+      end
+      #log.debug "Ended up with #{current_ordered_reads.length} reads that should be present next time"
+    end
+  end
+
+  class PileupRead
+    # Directions relative to reference
+    FORWARD_DIRECTION = '+'
+    REVERSE_DIRECTION = '-'
+
+    # sequence is always in the direction of the start of the reference to the end - only @direction gives direction information
+    attr_accessor :direction, :sequence
+    
+    # A hash of recorded insertions. Key of hash is the position in the consensus that is has been added to in the alignment, value is the bases that have been inserted
+    attr_reader :insertions
+    
+    def initialize
+      @sequence = ''
+      @insertions = {}
+    end
+    
+    def read
+      @sequence[@sequence.length-2..@sequence.length-1]
+    end
+    
+    def add_insertion(position, insertion_length, insertion_bases)
+      insertions[position] = insertion_bases
+    end
+  end
+end

data/test/helper.rb

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-pileup_iterator'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-pileup_iterator.rb

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+require 'helper'
+
+class TestBioPileupIterator < Test::Unit::TestCase
+  def test_pileup_parsing
+    line = "contig00001\t199\tA\t4\t.$...$\t>a^>"
+    #contig00001\t200\tT\t2\t..\taR"
+    piles = Bio::DB::PileupIterator.new(line).to_a
+    pileup = piles[0]
+    reads = piles[0].reads
+
+    assert_equal 'A', reads[0].sequence
+    assert_equal 4, reads.length
+    assert_kind_of Bio::DB::Pileup, pileup
+  end
+
+  def test_2_pileup_columns
+    line = "contig00001\t199\tA\t4\t.$...$\t>a^>\ncontig00001\t200\tT\t2\t..\taR"
+    piles = Bio::DB::PileupIterator.new(line).to_a
+
+    pileup = piles[0]
+    reads = piles[0].reads
+    reads2 = piles[1].reads
+
+    assert_equal 'A', piles[0].ref_base
+    assert_equal 'T', piles[1].ref_base
+    assert_equal 4, reads.length
+    assert_equal 2, reads2.length
+    assert_equal 'AT', reads2[0].sequence
+  end
+
+  def test_fwd_rev
+    line = "contig00001\t199\tA\t4\t.$,..$\t>a^>\ncontig00001\t200\tT\t2\t,.\taR"
+    piles = Bio::DB::PileupIterator.new(line).to_a
+
+    pileup = piles[0]
+    reads = piles[0].reads
+    reads2 = piles[1].reads
+
+    assert_equal 4, reads.length
+    assert_equal 2, reads2.length
+    assert_equal 'AT', reads2[0].sequence
+    assert_equal '-', reads2[0].direction
+    assert_equal '+', reads2[1].direction
+  end
+
+  def test_deletion
+    line = "contig00001\t199\tA\t4\t.-1T...$\t>a^>\ncontig00001\t200\tT\t2\t*..\taR"
+    piles = Bio::DB::PileupIterator.new(line).to_a
+
+    pileup = piles[0]
+    reads = piles[0].reads
+    reads2 = piles[1].reads
+
+    assert_equal 'A*', reads[0].sequence
+    assert_equal Hash.new, reads[0].insertions
+  end
+
+  def test_substitution
+    line = "contig00001\t199\tA\t4\t.G..$\t>a^>"
+    piles = Bio::DB::PileupIterator.new(line).to_a
+
+    pileup = piles[0]
+    reads = piles[0].reads
+
+    assert_equal 'A', reads[0].sequence
+    assert_equal 'G', reads[1].sequence
+    assert_equal 'A', reads[0].sequence
+  end
+
+  def test_substitution_with_insertion
+    line = "contig00001\t199\tA\t4\tG-1T..$.\t>a^>\ncontig00001\t200\tT\t2\t*..\taR"
+    piles = Bio::DB::PileupIterator.new(line).to_a
+
+    pileup = piles[0]
+    reads = piles[0].reads
+    reads2 = piles[1].reads
+
+    assert_equal 2, piles.length
+    assert_equal 4, reads.length
+    assert_equal 3, reads2.length
+    assert_equal 'G*', reads[0].sequence
+    assert_equal 'AT', reads[1].sequence
+    assert_equal 'A', reads[2].sequence
+    assert_equal 'AT', reads[3].sequence
+  end
+
+  def test_start_read_warning_of_deletion_next
+    line = "contig00001\t8\tG\t4\t..,^],-1g\ta!U!\n"+
+    "contig00001\t9\tg\t4\t..,*\ta!aU"
+    piles = Bio::DB::PileupIterator.new(line).to_a
+
+    pileup = piles[0]
+    reads = piles[0].reads
+    reads2 = piles[1].reads
+  end
+  
+  def test_star_then_insert
+    line = "contig00001\t23\tC\t40\t.*+1G..\t~~~~\n"
+    piles = Bio::DB::PileupIterator.new(line).to_a
+    
+    pileup = piles[0]
+    reads = piles[0].reads
+    
+    assert_equal 4, reads.length
+    assert_equal({}, reads[0].insertions)
+    assert_equal '*', reads[1].sequence
+    assert_equal({23 => 'G'}, reads[1].insertions)
+  end
+  
+  def test_star_finishing_a_read
+    line = "contig00001\t717\tC\t47\t,$.$,$*$,$,$,$,$,$,$,$*$*$*$*$,$.$*$*$*$*$.$.$.$,$,$*$,$,$,$,$.$.$*$*$.$,$,$,$,$.$,$.$,$*$,$,$\t0..~2-.-.,#~~~~+,~~~~+**,!~!!!!!!~~(((((((((~!!\n"
+    piles = Bio::DB::PileupIterator.new(line).to_a
+    assert_equal '*', piles[0].reads[3].sequence
+  end
+  
+  def test_start_finishing_a_read
+    line = "contig00002\t1\tC\t47\t^],$\t~\n"
+    piles = Bio::DB::PileupIterator.new(line).to_a
+    assert_equal 'C', piles[0].reads[0].sequence
+  end
+  
+  def test_start_with_a_gap
+    line = "contig00075\t503\tT\t24\t,^]*\tU\n"
+    piles = Bio::DB::PileupIterator.new(line)
+    # piles.log.level = Bio::Log::DEBUG
+    piles = piles.to_a
+    assert_equal 'T', piles[0].reads[0].sequence
+    assert_equal '*', piles[0].reads[1].sequence
+  end
+
+  def test_start_then_insert_then_end
+    line = "contig00075\t503\tG\t24\t^].+1T$^].\t~~\n"
+    piles = Bio::DB::PileupIterator.new(line)
+    # piles.log.level = Bio::Log::DEBUG
+    piles = piles.to_a
+    assert_equal 'G', piles[0].reads[0].sequence
+    assert_equal({503 => 'T'}, piles[0].reads[0].insertions)
+    assert_equal 'G', piles[0].reads[1].sequence
+  end
+
+  def test_star_then_insert2
+    line = "contig00075\t503\tG\t24\t,*+1g.\t~~\n"
+    piles = Bio::DB::PileupIterator.new(line)
+    # piles.log.level = Bio::Log::DEBUG
+    piles = piles.to_a
+    assert_equal 'G', piles[0].reads[0].sequence
+    assert_equal '*', piles[0].reads[1].sequence
+    assert_equal 'G', piles[0].reads[2].sequence
+  end
+  
+  def test_start_with_gap_then_insertion
+    line = "contig00075\t503\tG\t24\t,,.^]*+1g\tE~\n"+
+    "contig00075\t504\tA\t24\t,,.,\tE~\n"
+    
+    piles = Bio::DB::PileupIterator.new(line)
+    # piles.log.level = Bio::Log::DEBUG
+    piles = piles.to_a
+    assert_equal 'GA', piles[0].reads[0].sequence
+    assert_equal 'GA', piles[0].reads[1].sequence
+    assert_equal 'GA', piles[0].reads[2].sequence
+    assert_equal '*A', piles[0].reads[3].sequence
+    assert_equal({503 => 'g'}, piles[0].reads[3].insertions)
+  end
+  
+  def test_double_insertion
+    line = "contig00075\t503\tG\t24\t*+1gg\tE\n"
+    
+    piles = Bio::DB::PileupIterator.new(line)
+    # piles.log.level = Bio::Log::DEBUG
+    piles = piles.to_a
+    assert_equal({503 => 'gg'}, piles[0].reads[0].insertions)
+  end
+  
+  def test_non_perfect_starting_read
+    line = "contig00075\t503\tG\t24\t^F.*+1gg\tE\n"
+    
+    piles = Bio::DB::PileupIterator.new(line)
+    # piles.log.level = Bio::Log::DEBUG
+    piles = piles.to_a
+    assert_equal '+', piles[0].reads[0].direction
+    assert_equal 'G', piles[0].reads[0].sequence
+    assert_equal '*', piles[0].reads[1].sequence
+  end
+  
+  def test_non_matching_finish
+    line = "contig00002\t6317\tC\t2\ta$.\t!B\n"+
+     "contig00002\t6318\tT\t1\t.\tA\n"
+
+    
+    piles = Bio::DB::PileupIterator.new(line)
+    # piles.log.level = Bio::Log::DEBUG
+    piles = piles.to_a
+    assert_equal 2, piles[0].reads.length
+    assert_equal 'a', piles[0].reads[0].sequence
+    assert_equal 'CT', piles[0].reads[1].sequence
+  end
+  
+  def test_insertion_then_mismatch
+    line = "contig00044\t867\tC\t6\t,,,,,.\t!:!!:=\n"+
+     "contig00044\t868\tG\t6\tt,+1ttt,.\t!A!!C9\n"
+
+    piles = Bio::DB::PileupIterator.new(line)
+    
+    piles = piles.to_a
+    assert_equal 6, piles[0].reads.length
+    assert_equal 'Ct', piles[0].reads[0].sequence
+    assert_equal 'CG', piles[0].reads[1].sequence
+    hash = {868=>'t'}
+    assert_equal hash, piles[0].reads[1].insertions
+    assert_equal 'Ct', piles[0].reads[2].sequence
+  end
+end

metadata

@@ -0,0 +1,160 @@
+--- !ruby/object:Gem::Specification
+name: bio-pileup_iterator
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Ben J. Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-05-17 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &84151300 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: *84151300
+- !ruby/object:Gem::Dependency
+  name: bio-samtools
+  requirement: &84150960 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.5.3
+  type: :runtime
+  prerelease: false
+  version_requirements: *84150960
+- !ruby/object:Gem::Dependency
+  name: bio-logger
+  requirement: &84150510 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *84150510
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: &84150270 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *84150270
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &84166240 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *84166240
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &84165520 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *84165520
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &84165000 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+  type: :development
+  prerelease: false
+  version_requirements: *84165000
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &84164380 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: *84164380
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: &84163460 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: *84163460
+description: Iterate through a samtools pileup file
+email: donttrustben near gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/bio-pileup_iterator.rb
+- lib/bio/db/pileup_iterator.rb
+- test/helper.rb
+- test/test_bio-pileup_iterator.rb
+homepage: http://github.com/wwood/bioruby-pileup_iterator
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -115500147
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.17
+signing_key: 
+specification_version: 3
+summary: Iterate through a samtools pileup file
+test_files: []