bio-polyploid-tools 0.8.3 → 0.8.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: e9acfc190624dec8c4d6e1831c71524c330ffdd2
-  data.tar.gz: 4307bf90f54200f65972ea596f94048d65edbcb1
+SHA256:
+  metadata.gz: 728d9fb436e9e7d26698d011179da63ba79fc45c40b0a771cafc5f4dc6d84bc3
+  data.tar.gz: 3c62bd8bcfcb5d3f460729f19f8382bd46c7821fcacb83d01b0ff3f336b38f1b
 SHA512:
-  metadata.gz: 7b7f9875c56e9395d4c934b456b2332218d3a4e202addd1cab48adcb0c443ad9cef607452ee4ed8ff32994cd4c10bc2cd10b3b24f966de49c02657a961d0d3d0
-  data.tar.gz: a445e30d15f958c54424300250a481e470c47284f3842ba0a285138527f14cd0baaeb30547abf6f8fdd52c5c742e81b0cc875cbf783c6664fdd72c5d950bdcca
+  metadata.gz: 99784b38c37f00e71c3c1fa07899ccca8e32b6ff27fc363bcece989e788c0db745a7db4ae566efb42b55742fd01e5a99adeb211a7d46029f6c148dba8e91e92a
+  data.tar.gz: 40f0990a5652374ea3bef3b0e8777882720626e33fdc448ff48c5f71141b87ce153680a0215ad95e13595ddead39db822d276911baf0647723cc7e8bf3195bdb

data/.travis.yml

@@ -9,6 +9,7 @@ addons:
     - exonerate  
 before_install:
   - gem update --system
+  - export RUBYOPT="-W1"
 rvm:
   - 2.1.10
   - 2.2.5
@@ -16,5 +17,4 @@ rvm:
   - 2.4.2
   - 2.5.0
 
-before_install:
-  - export RUBYOPT="-W1"
+

data/Gemfile

@@ -5,6 +5,7 @@ source "http://rubygems.org"
 
 gem "bio", ">= 1.5.1"
 gem "bio-samtools", ">= 2.6.2"
+gem "descriptive_statistics"
 #gem "rake"
 
 gem "systemu", ">=2.5.2"

data/README.md

@@ -128,6 +128,14 @@ To use blast instead of exonerate, use the following command:
 
 ## Release Notes
 
+### 0.8.4 
+
+* Added script ```tag_stats.rb`` That gets the descriptive statistics for a tag in a bam file for each reference. 
+
+```bash
+ruby tag_stats.rb -b HI.3206.006.Index_2.CS_125RNA_14d_Leaf8.sorted.bam -r /Users/ramirezr/Dropbox/JIC/expVIPMetadatas/RefSeq1.0/Genes/annotation/IWGSCv1.0_UTR_ALL.cdnas.fasta --tag 'NH'
+```
+
 ### 0.8.3
 
 * BUGFIX: ```ChromosomeArm.rb``` was fixed to conform the module assumptions for the package. 
@@ -171,8 +179,6 @@ To use blast instead of exonerate, use the following command:
 
 # Notes
 
-
-* BUG: If the SNP is in a gap in the alignment to the chromosomes, it is ignored. 
 * BUG: Blocks with NNNs are picked and treated as semi-specific. 
 * BUG: If the name of the reference have space, the ID is not chopped. ">gene_1 (G12A)" shouls be treated as ">gene_1". 
 * TODO: Add a parameter file to configure the alignments. 

data/VERSION

@@ -1 +1 @@
-0.8.3
+0.8.4

data/bin/mask_triads.rb

@@ -0,0 +1,169 @@
+#!/usr/bin/env ruby
+require 'optparse'
+
+require 'csv'
+require 'fileutils'
+require 'tmpdir'
+require 'bio-samtools'
+require 'bio'
+
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
+require path
+opts = {}
+opts[:identity] = 50
+opts[:min_bases] = 200
+opts[:split_token] = "."
+opts[:tmp_folder]  = Dir.mktmpdir
+opts[:random_sample] = 0
+opts[:output_folder] = "."
+
+OptionParser.new do |o|
+
+  o.banner = "Usage: mask_triads.rb [options]"
+
+  o.on("-t", "--triads FILE", "CSV file with the gene triad names in the named columns 'A','B' and 'D' ") do |o|
+    opts[:triads] = o
+  end
+
+  o.on("-f", "--fasta FILE" , "FASTA file containing all the possible peptide sequences. ") do |o|
+    opts[:fasta] = o
+  end
+
+  o.on("-s", "--split_token CHAR", "Character used to split the sequence name. The name will be evarything before this token on the name of the sequences") do |o|
+    opts[:split_token] = o
+  end
+
+  o.on("-o", "--output_folder DIR", "Location to save the alignment masks. If the alignment exists, it is recycled to avoid calling MAFFT again") do |o|
+    opts[:output_folder] = o
+  end
+end.parse!
+
+
+split_token = opts[:split_token]
+reference_name = File.basename opts[:fasta]
+output_folder = opts[:output_folder]
+@fasta_reference_db = Bio::DB::Fasta::FastaFile.new(fasta: opts[:fasta])
+@fasta_reference_db.load_fai_entries
+#puts @fasta_reference_db.index.entries
+@cannonical = Hash.new
+@fasta_reference_db.index.entries.each do |e|
+  gene = e.id.split(split_token)[0]
+  @cannonical[gene] = e unless @cannonical[gene]
+  @cannonical[gene]  = e if   e.length > @cannonical[gene].length
+end
+
+$stderr.puts "#Loaded #{@cannonical.length} canonical sequences from #{@fasta_reference_db.index.size} in reference"
+
+$stderr.puts "TMP dir: #{opts[:tmp_folder]}"
+
+def write_fasta_from_hash(sequences, filename)
+  out = File.new(filename, "w")
+  sequences.each_pair do | chromosome, exon_seq |
+    out.puts ">#{chromosome}\n#{exon_seq}\n"
+  end
+  out.close
+end
+
+def mafft_align(a, b, d)
+  to_align = Bio::Alignment::SequenceHash.new
+  seq_a = @fasta_reference_db.fetch_sequence(@cannonical[a].get_full_region)
+  seq_b = @fasta_reference_db.fetch_sequence(@cannonical[b].get_full_region)
+  seq_d = @fasta_reference_db.fetch_sequence(@cannonical[d].get_full_region)
+  to_align[a] = seq_a
+  to_align[b] = seq_b
+  to_align[d] = seq_d
+  report = mafft.query_alignment(to_align)
+  aln = report.alignment
+  aln
+end
+
+def read_alignment(path)
+  aln = Bio::Alignment::SequenceHash.new
+  i = 0
+  Bio::FlatFile.open(Bio::FastaFormat, path) do |fasta_file|
+    fasta_file.each do |entry|
+      aln[entry.entry_id] = entry.seq if i < 3
+      i += 1
+    end
+  end
+  aln
+end
+
+
+mafft_opts = ['--maxiterate', '1000', '--localpair', '--quiet']
+mafft = Bio::MAFFT.new( "mafft" , mafft_opts)
+header_printed = false
+stats     = File.open("#{output_folder}/#{reference_name}.identity_stats.csv", "w")
+distances = File.open("#{output_folder}/#{reference_name}.distance_between_snps.csv.gz", "w")
+gz = Zlib::GzipWriter.new(distances)
+gz.write "triad,gene,genome,reference,type,distance\n"
+#gz.close
+
+def write_distances(distances, triad, gene, genome, reference, type, out)
+  distances.each { |e| out.write "#{triad},#{gene},#{genome},#{reference},#{type},#{e}\n" }
+end
+
+i = 0
+CSV.foreach(opts[:triads], headers:true ) do |row|
+  next unless row["cardinality_abs"] == "1:1:1" and row["HC.LC"] == "HC-only"
+   a = row['A']
+   b = row['B']
+   d = row['D']
+   triad = row['group_id']
+   cent_triad = triad.to_i / 100
+   folder = "#{output_folder}/alignments/#{reference_name}/#{cent_triad}/"
+   save_cds = "#{folder}/#{triad}.fa"
+   aligned = File.file?(save_cds)
+   aln = aligned ? read_alignment(save_cds)  : mafft_align(a,b,d)
+   folder = "#{output_folder}/alignments_new/#{reference_name}/#{cent_triad}/" if aligned
+   FileUtils.mkdir_p folder
+   save_cds = "#{folder}/#{triad}.fa"
+
+   aln2 = Bio::Alignment.new aln
+   seq_start = Bio::PolyploidTools::Mask.find_start(aln)
+   seq_end   = Bio::PolyploidTools::Mask.find_end(aln)
+   #puts "#{triad}: #{seq_start}-#{seq_end}"
+
+
+   aln2.add_seq(Bio::PolyploidTools::Mask.get(aln,seq_start: seq_start, seq_end: seq_end, target: a), "A")
+   aln2.add_seq(Bio::PolyploidTools::Mask.get(aln,seq_start: seq_start, seq_end: seq_end, target: b), "B")
+   aln2.add_seq(Bio::PolyploidTools::Mask.get(aln,seq_start: seq_start, seq_end: seq_end, target: d), "D")
+
+   a_stats =  Bio::PolyploidTools::Mask.stats(aln2["A"], triad, a, "A", reference_name)
+   b_stats =  Bio::PolyploidTools::Mask.stats(aln2["B"], triad, b, "B", reference_name)
+   d_stats =  Bio::PolyploidTools::Mask.stats(aln2["D"], triad, d, "D", reference_name)
+  
+   write_distances(a_stats[:specific], triad, a, "A", reference_name, "specific", gz)
+   write_distances(b_stats[:specific], triad, b, "B", reference_name, "specific", gz)
+   write_distances(d_stats[:specific], triad, d, "D", reference_name, "specific", gz)
+
+   write_distances(a_stats[:semispecific], triad, a, "A", reference_name, "semispecific", gz)
+   write_distances(b_stats[:semispecific], triad, b, "B", reference_name, "semispecific", gz)
+   write_distances(d_stats[:semispecific], triad, d, "D", reference_name, "semispecific", gz)
+   
+   a_stats.delete(:semispecific)
+   b_stats.delete(:semispecific)
+   d_stats.delete(:semispecific)
+   
+   a_stats.delete(:specific)
+   b_stats.delete(:specific)
+   d_stats.delete(:specific)
+
+   a_stats[:length] = @cannonical[a].length
+   b_stats[:length] = @cannonical[b].length
+   d_stats[:length] = @cannonical[d].length
+
+   stats.puts a_stats.keys.join(",") unless header_printed
+   stats.puts a_stats.values.join(",")
+   stats.puts b_stats.values.join(",")
+   stats.puts d_stats.values.join(",")
+   header_printed = true
+
+   write_fasta_from_hash(aln2, save_cds)
+   i += 1
+end
+gz.close
+distances.close
+stats.close

data/bin/polymarker.rb

@@ -350,10 +350,11 @@ container.add_alignments({
 
 
 #4.1 generating primer3 file
-write_status "Running primer3"
+write_status "Finding genome-specific positions"
 file = File.open(exons_filename, "w")
 container.print_fasta_snp_exones(file)
 file.close
+write_status "Running primer3"
 
 file = File.open(primer_3_input, "w")
 

data/bin/tag_stats.rb

@@ -0,0 +1,75 @@
+#!/usr/bin/env ruby
+require 'optparse'
+
+require 'csv'
+require 'fileutils'
+require 'tmpdir'
+require 'bio-samtools'
+require 'bio'
+require 'descriptive_statistics'
+
+class Bio::DB::Tag
+  def set(str) 
+    @tag   = str[0..1]
+    @type  = str[3]
+    @value = str[5..-1]
+    @value = @value.to_i if @type == "i"
+  end
+end
+
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
+require path
+opts = {}
+opts[:tag] = "NH"
+opts[:bam] = nil
+opts[:out] = nil
+opts[:ref] = nil
+
+out = $stdout
+
+OptionParser.new do |o|
+  o.banner = "Usage: tag_stats.rb [options]"
+
+  o.on("-t", "--tag str", "The tag to extract (default NH)") do |o|
+    opts[:tag] = o
+  end
+
+  o.on("-b", "--bam FILE" , "BAM file with the alignments ") do |o|
+    opts[:bam] = o
+  end
+
+  o.on("-o", "--out_file CHAR", "File to save the stats") do |o|
+    opts[:out] = o
+  end
+  
+  o.on("-r", "--reference FILE", "Fasta file with the reference") do |o|
+    opts[:ref] = o
+  end
+end.parse!
+
+bam =  Bio::DB::Sam.new(fasta: opts[:ref], bam: opts[:bam])
+tag = opts[:tag]
+
+sample = File.basename(opts[:bam], '.sorted.bam')
+last_ref = ""
+values = []
+to_print = [:sum, :min, :max, :mean, :mode, :median, :q1, :q2, :q3]
+percentiles = [90, 95, 97.5, 99]
+#Add the 90, 95, 97.5 and 99 percentiles.
+out = File.open(opts[:out], "w")  if opts[:out]
+bam.view do |aln |
+  if(last_ref != aln.rname)
+    
+    desc_stats = values.descriptive_statistics
+    to_print.each    { |e| out.puts [sample, last_ref, e      , desc_stats[e]       ].join("\t")  } if(last_ref !=  "")
+    percentiles.each { |e| out.puts [sample, last_ref, "P#{e}", values.percentile(e)].join("\t")  } if(last_ref !=  "")
+    out.puts [sample, last_ref, "N", values.length].join("\t") if(last_ref !=  "")
+    values.clear
+    last_ref = aln.rname  
+  end
+  values << aln.tags[tag].value
+end
+
+out.close  if opts[:out]

data/bio-polyploid-tools.gemspec

@@ -2,19 +2,19 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.8.3 ruby lib
+# stub: bio-polyploid-tools 0.8.4 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.8.3"
+  s.version = "0.8.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Ricardo H.  Ramirez-Gonzalez".freeze]
-  s.date = "2018-01-23"
+  s.date = "2018-02-27"
   s.description = "Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat".freeze
   s.email = "ricardo.ramirez-gonzalez@jic.ac.uk".freeze
-  s.executables = ["bfr.rb".freeze, "blast_triads.rb".freeze, "blast_triads_promoters.rb".freeze, "count_variations.rb".freeze, "filter_blat_by_target_coverage.rb".freeze, "filter_exonerate_by_identity.rb".freeze, "find_best_blat_hit.rb".freeze, "find_best_exonerate.rb".freeze, "find_homoeologue_variations.rb".freeze, "get_longest_hsp_blastx_triads.rb".freeze, "hexaploid_primers.rb".freeze, "homokaryot_primers.rb".freeze, "mafft_triads.rb".freeze, "mafft_triads_promoters.rb".freeze, "map_markers_to_contigs.rb".freeze, "markers_in_region.rb".freeze, "polymarker.rb".freeze, "polymarker_capillary.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "vcfLineToTable.rb".freeze]
+  s.executables = ["bfr.rb".freeze, "blast_triads.rb".freeze, "blast_triads_promoters.rb".freeze, "count_variations.rb".freeze, "filter_blat_by_target_coverage.rb".freeze, "filter_exonerate_by_identity.rb".freeze, "find_best_blat_hit.rb".freeze, "find_best_exonerate.rb".freeze, "find_homoeologue_variations.rb".freeze, "get_longest_hsp_blastx_triads.rb".freeze, "hexaploid_primers.rb".freeze, "homokaryot_primers.rb".freeze, "mafft_triads.rb".freeze, "mafft_triads_promoters.rb".freeze, "map_markers_to_contigs.rb".freeze, "markers_in_region.rb".freeze, "mask_triads.rb".freeze, "polymarker.rb".freeze, "polymarker_capillary.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "tag_stats.rb".freeze, "vcfLineToTable.rb".freeze]
   s.extra_rdoc_files = [
     "README",
     "README.md"
@@ -42,10 +42,12 @@ Gem::Specification.new do |s|
     "bin/mafft_triads_promoters.rb",
     "bin/map_markers_to_contigs.rb",
     "bin/markers_in_region.rb",
+    "bin/mask_triads.rb",
     "bin/polymarker.rb",
     "bin/polymarker_capillary.rb",
     "bin/snp_position_to_polymarker.rb",
     "bin/snps_between_bams.rb",
+    "bin/tag_stats.rb",
     "bin/vcfLineToTable.rb",
     "bio-polyploid-tools.gemspec",
     "conf/defaults.rb",
@@ -88,6 +90,7 @@ Gem::Specification.new do |s|
     "lib/bio/PolyploidTools/ChromosomeArm.rb",
     "lib/bio/PolyploidTools/ExonContainer.rb",
     "lib/bio/PolyploidTools/Marker.rb",
+    "lib/bio/PolyploidTools/Mask.rb",
     "lib/bio/PolyploidTools/NoSNPSequence.rb",
     "lib/bio/PolyploidTools/PrimerRegion.rb",
     "lib/bio/PolyploidTools/SNP.rb",
@@ -172,7 +175,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "2.6.14".freeze
+  s.rubygems_version = "2.7.4".freeze
   s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze
 
   if s.respond_to? :specification_version then
@@ -181,6 +184,7 @@ Gem::Specification.new do |s|
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<bio>.freeze, [">= 1.5.1"])
       s.add_runtime_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])
+      s.add_runtime_dependency(%q<descriptive_statistics>.freeze, [">= 0"])
       s.add_runtime_dependency(%q<systemu>.freeze, [">= 2.5.2"])
       s.add_development_dependency(%q<shoulda>.freeze, [">= 2.10"])
       s.add_development_dependency(%q<test-unit>.freeze, [">= 0"])
@@ -188,6 +192,7 @@ Gem::Specification.new do |s|
     else
       s.add_dependency(%q<bio>.freeze, [">= 1.5.1"])
       s.add_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])
+      s.add_dependency(%q<descriptive_statistics>.freeze, [">= 0"])
       s.add_dependency(%q<systemu>.freeze, [">= 2.5.2"])
       s.add_dependency(%q<shoulda>.freeze, [">= 2.10"])
       s.add_dependency(%q<test-unit>.freeze, [">= 0"])
@@ -196,6 +201,7 @@ Gem::Specification.new do |s|
   else
     s.add_dependency(%q<bio>.freeze, [">= 1.5.1"])
     s.add_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])
+    s.add_dependency(%q<descriptive_statistics>.freeze, [">= 0"])
     s.add_dependency(%q<systemu>.freeze, [">= 2.5.2"])
     s.add_dependency(%q<shoulda>.freeze, [">= 2.10"])
     s.add_dependency(%q<test-unit>.freeze, [">= 0"])

data/lib/bio/PolyploidTools/Mask.rb

@@ -0,0 +1,114 @@
+class Array
+  def sum
+    inject(0.0) { |result, el| result + el }
+  end
+
+  def mean
+    sum / size
+  end
+end
+
+module Bio::PolyploidTools::Mask
+
+  def self.find_end(seqs)
+    size = seqs.values[0].size
+    names = seqs.keys
+    i = size - 1
+    gap_count = 3
+    while i > 0 and gap_count > 0
+      gap_count = names.map { |chr| seqs[chr][i] == "-" ? 1:0  }.inject(0, :+)
+      i -= 1
+    end
+    i + 1
+  end
+
+  def self.find_start(seqs)
+    size = seqs.values[0].size
+    names = seqs.keys
+    i = 0
+    gap_count = 3
+    while i < size  and gap_count > 0
+      gap_count = names.map { |chr| seqs[chr][i] == "-" ? 1 : 0  } .inject(0, :+)
+
+      i += 1
+    end
+    i - 1
+  end
+
+  def self.get(seqs, target: nil, seq_start: 0, seq_end: 0)
+    names = seqs.keys
+    target = names[0] if target.nil?
+    masked_snps = seqs[target].downcase
+    i = 0
+    while i < masked_snps.size
+      different = 0
+      cov = 0
+      gap = false
+      names.each do | chr |
+        if seqs[chr][i]  != "-" and seqs[chr][i]  != "n" and seqs[chr][i]  != "N"
+          cov += 1
+        end
+        if chr != target
+         different += 1  if masked_snps[i].upcase != seqs[chr][i].upcase
+        end
+        if seqs[chr][i]  == "-" and chr == target
+            gap = true
+        end
+      end
+      masked_snps[i] = "." if different == 0
+      masked_snps[i] = "." if cov == 1
+      masked_snps[i] = "*" if cov == 0
+      expected_snps  = names.size - 1
+      masked_snps[i] = masked_snps[i].upcase if different == expected_snps
+      if gap
+        masked_snps[i] = different == expected_snps ? "-" : "_"
+      end
+      masked_snps[i] = "|" if i < seq_start or i > seq_end
+      i += 1
+    end
+    masked_snps
+  end
+
+  def self.stats(mask, triad, gene, genome, reference)
+    specific = []
+    semispecific = []
+    sp_i = 0
+    semi = 0
+    i = 0
+    mask.to_s.each_char do |e|
+      case e
+      when "n","N"
+        i += 1
+      when /[[:lower:]]/ then
+        semispecific << semi
+        semi = 0
+        i += 1
+      when /[[:upper:]]/ then
+        specific     << sp_i
+        semispecific << semi
+        sp_i = 0
+        semi = 0
+        i += 1
+      when "." then
+        semi += 1
+        sp_i += 1
+        i += 1
+      end
+    end
+    {
+      reference: reference,
+      triad: triad,
+      genome: genome,
+      gene: gene,
+      semispecific_mean: semispecific.mean,
+      semispecific_bases: semispecific.size,
+      semispecific_identity: (1 - (semispecific.size.to_f / i)) * 100 ,
+      specific_mean: specific.mean,
+      specific_bases: specific.size,
+      specific_identity: (1 - (specific.size.to_f / i )) * 100,
+      aligned_length: i,
+      specific: specific,
+      semispecific: semispecific
+    }
+  end
+end

data/lib/bio/PolyploidTools/SNPSequence.rb

@@ -33,10 +33,6 @@ module Bio::PolyploidTools
       snp
     end
     
-    def parse_snp
-      
-    end
-
     def parse_sequence_snp
       pos = 0
       match_data = /(?<pre>\w*)\[(?<org>[ACGT])\/(?<snp>[ACGT])\](?<pos>\w*)/.match(sequence_original.strip)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.8.3
+  version: 0.8.4
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-01-23 00:00:00.000000000 Z
+date: 2018-02-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -38,6 +38,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 2.6.2
+- !ruby/object:Gem::Dependency
+  name: descriptive_statistics
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: systemu
   requirement: !ruby/object:Gem::Requirement
@@ -114,10 +128,12 @@ executables:
 - mafft_triads_promoters.rb
 - map_markers_to_contigs.rb
 - markers_in_region.rb
+- mask_triads.rb
 - polymarker.rb
 - polymarker_capillary.rb
 - snp_position_to_polymarker.rb
 - snps_between_bams.rb
+- tag_stats.rb
 - vcfLineToTable.rb
 extensions: []
 extra_rdoc_files:
@@ -146,10 +162,12 @@ files:
 - bin/mafft_triads_promoters.rb
 - bin/map_markers_to_contigs.rb
 - bin/markers_in_region.rb
+- bin/mask_triads.rb
 - bin/polymarker.rb
 - bin/polymarker_capillary.rb
 - bin/snp_position_to_polymarker.rb
 - bin/snps_between_bams.rb
+- bin/tag_stats.rb
 - bin/vcfLineToTable.rb
 - bio-polyploid-tools.gemspec
 - conf/defaults.rb
@@ -192,6 +210,7 @@ files:
 - lib/bio/PolyploidTools/ChromosomeArm.rb
 - lib/bio/PolyploidTools/ExonContainer.rb
 - lib/bio/PolyploidTools/Marker.rb
+- lib/bio/PolyploidTools/Mask.rb
 - lib/bio/PolyploidTools/NoSNPSequence.rb
 - lib/bio/PolyploidTools/PrimerRegion.rb
 - lib/bio/PolyploidTools/SNP.rb
@@ -293,7 +312,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.14
+rubygems_version: 2.7.4
 signing_key: 
 specification_version: 4
 summary: Tool to work with polyploids, NGS and molecular biology