bio-pileup_iterator 0.0.1 → 0.0.3

data/README.md

@@ -0,0 +1,69 @@
+# bio-pileup_iterator
+
+[Pileup format](http://samtools.sourceforge.net/pileup.shtml) files are a representation of an alignment/mapping of reads to a reference. This biogem builds on the [bio-samtools biogem](https://github.com/helios/bioruby-samtools) to create enable developers to iterate through columns of a pileup format file, and interrogate possible polymorphisms for e.g. SNP detection. Say we have the pile lines like so
+
+    contig00001	199	A	4	.$...$	>a^>
+    contig00001	200	T	2	..+1A	aR
+
+i.e.
+
+    line = "contig00001\t199\tA\t4\t.$...$\t>a^>\ncontig00001\t200\tT\t2\t..+1A\taR"
+
+Then
+
+    piles = Bio::DB::PileupIterator.new(line).to_a
+    piles[0].reads #=> An array of 4 pileup reads (Bio::DB::PileupIterator::PileupRead objects)
+
+The first reads ends at the first position
+
+    piles[0].reads[0].sequence #=> 'A'
+
+The second read covers both positions:
+
+    piles[0].reads[1].sequence #=> 'AT'
+
+Note that when you don't use ```to_a```, instead using ```Bio::DB::PileupIterator#each```, there is no "lookahead" (yet), so it doesn't find the T before it has iterated over it:
+
+    Bio::DB::PileupIterator.new(line).each{|pile| puts pile.reads[1].sequence if pile.pos==199} #=> "A"
+
+Directions
+
+    piles[0].reads[1].direction #=> '+'
+
+Insertions
+
+    piles[1].reads[1].insertions #=> {200=>"A"}
+
+Apologies in advance for any missing features (e.g. currently it does handle deletions) and slowness (it wasn't really written with speed in mind).
+
+## Installation
+
+        gem install bio-pileup_iterator
+
+## 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/VERSION

@@ -1 +1 @@
-0.0.1
+0.0.3

data/lib/bio/db/pileup_iterator.rb

@@ -21,45 +21,42 @@ class Bio::DB::PileupIterator
   # 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']
+    logging = true
     
     @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}"
+      log.debug "new column's read_bases: #{bases.inspect}" if log.debug?
+      log.debug "pileup entry parsed: #{pileup.inspect}" if log.debug?
       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'
+          log.debug 'adding a new read: '+bases if log.debug?
           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 starting, remove it
+        matched_string = ''
+        if bases[0..1]=='^]'
+          matched_string += bases[0]
+          bases = bases[2...bases.length]
+        end
+        log.debug "after read start removal, pileup is #{bases}" if log.debug?
+        
+        # next expect the actual base bit
+        if matches = bases.match(/^([ACGTNacgtn\.\,\*])/)
+          matched_string += bases[0]
           if matches[1] == '.'
             raise if !current_read.direction.nil? and current_read.direction != PileupRead::FORWARD_DIRECTION
             current_read.direction = PileupRead::FORWARD_DIRECTION
@@ -72,152 +69,47 @@ class Bio::DB::PileupIterator
             # 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}"
+          # remove the matched base
+          bases = bases[1...bases.length]
+        else
+          raise Exception, "Expected a character corresponding to a base, one of '[ACGTNacgtn.,]'. Starting here: #{bases}, from #{pileup.inspect}"
+        end
+        log.debug "after regular position removal, pileup is #{bases}" if log.debug?
         
-        # 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
+        # then read insertion or deletion in the coming position(s)
+        if matches = bases.match(/^([\+\-])([0-9]+)/)
+          matched_length = matches[1].length+matches[2].length
+          bases = bases[matched_length...bases.length]
+          matched_string += matches[1]+matches[2]
+          log.debug "after removal of bases leading up to an insertion/deletion, pileup is #{bases}" if log.debug?
           
-          # 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
-
+          regex = /^([ACGTNacgtn=]{#{matches[2].to_i}})/
+          log.debug "insertion/deletion secondary regex: #{regex.inspect}" if log.debug?
+          last_matched = bases.match(regex)
           
-        # 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]}"
+          if last_matched.nil?
+            raise Exception, "Failed to parse insertion. Starting here: #{bases}, from #{pileup.inspect}"
           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
+            bases = bases[last_matched[1].length...bases.length]
+            if matches[1]=='+'
+              # record the insertion
+              current_read.add_insertion pileup.pos, matches[2], last_matched[1]
+            elsif matches[1]=='-'
+              #currently deletions are not recorded, slipped to future
+            end
           end
         end
-        #log.debug "current read's sequence: #{current_read.sequence}"
+        log.debug "after indel removal, pileup is now #{bases}" if log.debug?
         
-        #raise Exception, "implement mismatch parsing here!!!"
-        raise Exception, "Unexpected Pileup format bases, starting here: #{bases}, from #{pileup.inspect}" if matches.nil?
+        # Then read an ending read
+        if bases[0]=='$'
+          reads_ending.push current_read_index
+          matched_string += '$'
+          bases = bases[1...bases.length]
+        end
+        
+        log.debug "Matched '#{matched_string}', now the bases are '#{bases}'" if log.debug?
         
-        #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
 

data/test/test_bio-pileup_iterator.rb

@@ -1,80 +1,87 @@
 require 'helper'
 
 class TestBioPileupIterator < Test::Unit::TestCase
+  #enable debug logging for pileup_iterator
+  def setup
+    log_name = 'bio-pileup_iterator'
+    Bio::Log::CLI.logger('stderr')
+    #Bio::Log::CLI.configure(log_name) # when commented out no debug is printed out
+  end
+  
   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..$.\t>a^>\ncontig00001\t200\tT\t2\t*..\taR"
     piles = Bio::DB::PileupIterator.new(line).to_a
-
+  
     pileup = piles[0]
     reads = piles[0].reads
     reads2 = piles[1].reads
-
+  
     assert_equal 2, piles.length
     assert_equal 4, reads.length
     assert_equal 3, reads2.length
@@ -83,12 +90,12 @@ class TestBioPileupIterator < Test::Unit::TestCase
     assert_equal 'A', reads[2].sequence
     assert_equal 'AT', reads[3].sequence
   end
-
+  
   def test_start_read_warning_of_deletion_next
     line = "contig00001\t8\tG\t4\t..,^],-1g\ta!U!\n"+
     "contig00001\t9\tg\t4\t..,*\ta!aU"
     piles = Bio::DB::PileupIterator.new(line).to_a
-
+  
     pileup = piles[0]
     reads = piles[0].reads
     reads2 = piles[1].reads
@@ -122,26 +129,23 @@ class TestBioPileupIterator < Test::Unit::TestCase
   def test_start_with_a_gap
     line = "contig00075\t503\tT\t24\t,^]*\tU\n"
     piles = Bio::DB::PileupIterator.new(line)
-    # piles.log.level = Bio::Log::DEBUG
     piles = piles.to_a
     assert_equal 'T', piles[0].reads[0].sequence
     assert_equal '*', piles[0].reads[1].sequence
   end
-
+  
   def test_start_then_insert_then_end
     line = "contig00075\t503\tG\t24\t^].+1T$^].\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
@@ -153,7 +157,6 @@ class TestBioPileupIterator < Test::Unit::TestCase
     "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
@@ -163,19 +166,17 @@ class TestBioPileupIterator < Test::Unit::TestCase
   end
   
   def test_double_insertion
-    line = "contig00075\t503\tG\t24\t*+1gg\tE\n"
+    line = "contig00075\t503\tG\t24\t*+2gg\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"
+    line = "contig00075\t503\tG\t24\t^].*+2gg\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
@@ -185,10 +186,9 @@ class TestBioPileupIterator < Test::Unit::TestCase
   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
@@ -198,7 +198,7 @@ class TestBioPileupIterator < Test::Unit::TestCase
   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
@@ -209,4 +209,18 @@ class TestBioPileupIterator < Test::Unit::TestCase
     assert_equal hash, piles[0].reads[1].insertions
     assert_equal 'Ct', piles[0].reads[2].sequence
   end
+  
+  def test_some_beta_testing_bug
+    #<Bio::DB::Pileup:0x00000009d5e8d8 @ref_name="contig03007", @pos=658, @ref_base="a", @coverage=14.0, @read_bases="gg+1cG-1Ag+1c*+1aG-1A*+1a****g**+1A", @read_quals="!!!!~!~!!!!!!~", @ref_count=nil, @non_ref_count_hash=nil, @non_ref_count=nil> (Exception)
+    line = "contig03007\t658\ta\t14\tgg+1cG-1Ag+1c*+1aG-1A*+1a****g**+1A\t!!!!~!~!!!!!!~\n"
+    piles = Bio::DB::PileupIterator.new(line).to_a #parse, it should fail otherwise
+    assert_equal 14, piles[0].coverage
+  end
+  
+  def test_unexpected_equals
+    line = "contig00032\t264\tg\t10\t*+1=$.*+1c,.*+1c...,\t~^~^^~^^^W\n"
+    piles = Bio::DB::PileupIterator.new(line).to_a #parse, it should fail otherwise
+    assert_equal 10, piles[0].coverage
+    assert_equal 10, piles[0].reads.length
+  end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-pileup_iterator
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-17 00:00:00.000000000 Z
+date: 2012-08-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &84151300 !ruby/object:Gem::Requirement
+  requirement: &79398350 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *84151300
+  version_requirements: *79398350
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &84150960 !ruby/object:Gem::Requirement
+  requirement: &79397770 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 0.5.3
   type: :runtime
   prerelease: false
-  version_requirements: *84150960
+  version_requirements: *79397770
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &84150510 !ruby/object:Gem::Requirement
+  requirement: &79397240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: 1.0.0
   type: :runtime
   prerelease: false
-  version_requirements: *84150510
+  version_requirements: *79397240
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &84150270 !ruby/object:Gem::Requirement
+  requirement: &79396870 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *84150270
+  version_requirements: *79396870
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &84166240 !ruby/object:Gem::Requirement
+  requirement: &79396550 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *84166240
+  version_requirements: *79396550
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &84165520 !ruby/object:Gem::Requirement
+  requirement: &79396200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *84165520
+  version_requirements: *79396200
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &84165000 !ruby/object:Gem::Requirement
+  requirement: &79395820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -87,10 +87,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *84165000
+  version_requirements: *79395820
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &84164380 !ruby/object:Gem::Requirement
+  requirement: &79481120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,10 +98,10 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *84164380
+  version_requirements: *79481120
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &84163460 !ruby/object:Gem::Requirement
+  requirement: &79480630 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -109,20 +109,20 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *84163460
+  version_requirements: *79480630
 description: Iterate through a samtools pileup file
 email: donttrustben near gmail.com
 executables: []
 extensions: []
 extra_rdoc_files:
 - LICENSE.txt
-- README.rdoc
+- README.md
 files:
 - .document
 - .travis.yml
 - Gemfile
 - LICENSE.txt
-- README.rdoc
+- README.md
 - Rakefile
 - VERSION
 - lib/bio-pileup_iterator.rb
@@ -144,7 +144,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -115500147
+      hash: 421311475
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/README.rdoc

@@ -1,39 +0,0 @@
-= 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.
-