Module: Vardetect::Vc

Defined in:
lib/vardetect-vc.rb,
lib/vardetect-vc/lib.rb,
lib/vardetect-vc/version.rb,
lib/vardetect-vc/call_snv.rb,
lib/vardetect-vc/call_combine.rb,
lib/vardetect-vc/call_prepare.rb

Constant Summary collapse

VERSION = 
"0.0.5"

Class Method Summary collapse

Class Method Details

.analyse_combine(params) ⇒ Object 



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# File 'lib/vardetect-vc/call_combine.rb', line 169

def self.analyse_combine params
  

  # index columns
  idx = {}
  %w{snp vc st pos ref vc_a1 vc_a vc_het vc_dep vc_alt vc_r snp_ann snp_a snp_het snp_gc snp_clus st_ref st_a2 st_qua st_dep st_alt st_pos}.each_with_index do |i,index|
    idx[i.to_sym] = index
  end

  # constant
  snp_filter = 0.75
  alt_ratio = 0.1


  gcid = idx[:snp_gc]
  hid = idx[:snp_het] 
  depid= idx[:vc_dep]


  combine_file =params['com_out']
  analyse_file =params['out']
  f_list = File.open(combine_file,'r')
  out  = File.open(analyse_file,'w')

  all_list = []
  list = []

  het_list = []
  hom_list = []


  # filter all by gc score snp array 
  while str = f_list.gets
    # puts str
    v = str.strip.split(',')
    all_list<<v
    if v[gcid].to_f>snp_filter     
      list<<v
    end
  end

  # filter set of snp array 's het hom
  for i in list
    if i[hid]=='het'  
      het_list<<i
    else
      hom_list<<i
    end
  end



  out.puts "SNP Array overlap data "
  out.puts "Filter GC score at,#{snp_filter}"
  out.puts "Total snv,#{all_list.size}"
  out.puts "Total snv not pass filter,#{all_list.size-list.size}"
  out.puts "Total hetero snv,#{het_list.size}"
  out.puts "Total homo snv,#{hom_list.size}"



  vc_het_het = []
  vc_het_hom = []
  vc_hom_hom = []
  vc_hom_het = []

  vchid = getidx :vc_het
  vcrid = getidx :vc_r
  [vchid]=='het' or
  for i in list

    if i[hid]=='het'
      if  i[vcrid].to_f >= alt_ratio
        vc_het_het<<i
      else
        vc_het_hom<<i
      end  
    else
      if  i[vcrid].to_f >= alt_ratio
        vc_hom_het<<i
      else
        vc_hom_hom<<i
      end  
    end
  end


  # matrix=[[vc_het_het.size,vc_het_hom.size],[vc_hom_hom.size,vc_hom_het.size]]



  require 'erb'
  outtmp = File.open(analyse_file+".html",'w')

  template = ERB.new(File.open('index.html.erb','r').read)


  outtmp.puts template.result(binding)

  outtmp.close

  `open #{analyse_file+".html"}`



  out.close
  f_list.close
end

.call_combine_all(params) ⇒ Object 



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# File 'lib/vardetect-vc/call_combine.rb', line 5

def self.call_combine_all params
  # ====================================================================================================
  # 4. All comparison
  # ====================================================================================================
  
   map_vc = []
   map_st = {}
   map_snp = {}
   

   vc_file =params['vc_out']
   st_file =params['st_out']
   snp_file =params['snp_out']
   
   com_out =params['com_out']
   
   f_st = File.open(st_file,'r')
   f_vc = File.open(vc_file,'r')
   f_snp = File.open(snp_file,'r')
   
   com_output = File.open(com_out,'w')
   
   puts "Indexing SNP Array SNV"
   while str = f_snp.gets
     v = str.strip.split(',')
     map_snp[v[0]] = v
   end
   
   puts map_snp.keys[0..10]
   
   puts "Indexing SamTools SNV"
      while str = f_st.gets
        v = str.strip.split(',')
        map_st[v[0]] = v
      end
   
    puts map_st.keys[0..10]
      
      puts "Indexing VC SNV"
         while str = f_vc.gets
           v = str.split(',')
      
         
      
           # if (v[2]==v[3] and alt.to_f/dep > 0.1) or v[2]!=v[3]   
           #              map_vc<<v
           #            end
           #            
           # if (v[2]==v[3] and alt.to_f/dep > 0.1) or v[2]!=v[3]   
              map_vc<<v
            # end
           
           
         end
         
         puts map_vc.size
         
         # puts map_vc[0..10]
      
        
        
        
        
        # map_vc.sort!{|a,b| a[1].to_i<=>b[1].to_i }
            
            all=0
            vc_count=0  
            st_count=0
            vc_het_rate=0
            st_het_rate=0
            final = []
            
            
            for i in  map_vc
               pos = i[0]
               # puts pos
               if snp = map_snp[pos]
                 
            
                 vc_alt = i[5].to_i
                 vc_dep = i[4].to_i+vc_alt
                 
                 vc_alt_a = '-'
                 vc_het = 0
                 
                     
                 snp_rs = snp[1]
                 snp_a1 = snp[2]
                 snp_a2 = snp[3]
                 
                 snp_a = "#{snp_a1}/#{snp_a2}"
                 snp_het = 0 
                 snp_het = 1 if snp_a1!=snp_a2 
                 snp_gc = snp[4]
                 snp_clust = snp[5]
                 snp_cmp = 1
                 
                 snp_check = false
                 if snp_a.strip !='-/-' 
                 all+=1 
                 snp_check = true
                 end
                 st_check = false
                 
                 vc_het_t = 'hom'
                 snp_het_t = 'hom'
                 snp_het_t = 'het' if snp_a1!=snp_a2 
                 
                 vc_het_ratio = vc_alt.to_f/vc_dep
                 if vc_het_ratio >= 0.15
                   vc_alt_a = i[3] 
                   vc_het = 1
                   vc_het_t = 'het'
                 end
                      
                 str = "#{i[0]},#{i[1]},#{i[2]},#{i[2]}/#{vc_alt_a},#{vc_het_t},#{vc_dep},#{vc_alt},#{vc_het_ratio},"
                 str += "#{snp_rs},#{snp_a},#{snp_het_t},#{snp_gc},#{snp_clust},"
                 
                 
                 
                 
                 if st = map_st[pos]
                   st_het = 0 
                   st_het = 1 if st[5] =='het'
                   str += st[4..-1].join(",")
                    if st_het==snp_het and snp_check
                    st_het_rate+=1
                    st_check =true
                    end
                    st_count+=1
                 end
                 vc_check = false
                 vc_check = true if vc_het==snp_het and snp_check
               
                 if snp_check and vc_check
                   vc_het_rate+=1 
                 end 
                 vc_count+=1
                
                 cmp = [snp_check,vc_check,st_check,str]
                 
                 # final << cmp
                 com_output.puts cmp.join(',')
                 
                 
               end
            end
            
        
        puts "All #{all} is not -/-"
        
        puts "VC Hetero Rate : #{vc_het_rate}"
        
        puts "ST Hetero Rate : #{st_het_rate}"
   
   f_st.close
   f_vc.close
   f_snp.close
   com_output.close
   
  
end

.call_prepare_snp(params) ⇒ Object 



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# File 'lib/vardetect-vc/call_prepare.rb', line 35

def self.call_prepare_snp params
  # ====================================================================================================
  # 3. SNP preparing filtered chromosome
  # ====================================================================================================

  snp_array_file =params['snp']
  snp_file =params['snp_out']

  count = 0
  list = []
  start = false
  run = false

  file = File.open(snp_array_file,'r')
  output = File.open snp_file,'w'
  map = {}
  while str = file.gets #and count<100
    str.strip!
    if str=='[Data]' and !start
      start = true
    elsif start
      s = str.split
      if s[0] =='Sample' and !run
        run = true
      else

          key = "#{s[1]}-#{s[2]}"
           map[key] = s

      end

    end
    count+=1
  end
    # 
    map.keys.sort.each do |k|
        v = map[k]
        output.puts "#{k},"+v[3..-1].join(",")
    end

  output.close   



end

.call_prepare_st(params) ⇒ Object 



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# File 'lib/vardetect-vc/call_prepare.rb', line 6

def self.call_prepare_st params
  # ====================================================================================================
  # 2. ST preparing filtered chromosome
  # ====================================================================================================
  count = 0
  start = false
  sam_tool_file =params['st']
  snp_file =params['st_out']


  st_output = File.open(snp_file,'w')
  CSV.foreach(sam_tool_file) do |row|
   if start 

      i = row[0][3..-1]
      id = i.to_i
      id = i if id == 0
      key = "#{id}-#{row[1]}"
      st_output.puts key+","+row.join(",")

     count +=1
   else
     start=true
   end
  end
  st_output.close

end

.call_prepare_vc(params) ⇒ Object 



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# File 'lib/vardetect-vc/call_prepare.rb', line 81

def self.call_prepare_vc params

  vc_raw_file =params['vc_raw']
  vc_file =params['vc_out']

  count = 0
  list = []

  file = File.open(vc_raw_file,'r')
  output = File.open vc_file,'w'
  map = {}
  while str = file.gets #and count<100
    str.strip!
    s = str.split
    # puts str
    begin
    if str

        alt = s[6].to_i  
        dep = s[5].to_i + alt
        if ( alt.to_f/dep > 0.1) or s[2]!=s[3] 
          i = s[0][3..-1]
          key = "#{i}-#{s[1]}"
            map[key] = s
        end
      end
    rescue
      puts str
    end
  end
    # 
    map.keys.sort.each do |k|
        v = map[k]
        output.puts "#{k},"+v[2..-1].join(",")
    end
  output.close 
end

.call_sam_snv(sam, chr, chr_start, chr_stop, debug = nil) ⇒ Object 



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# File 'lib/vardetect-vc/call_snv.rb', line 42

def self.call_sam_snv sam,chr,chr_start,chr_stop, debug=nil
  
  unless debug
    show = false
    indel_show = false
    var_show = false
  else
      s = debug.split('|')
      show = s.index('show')
      indel_show =  s.index('indel')
      var_show =  s.index('var')
  end
 
  
  l = nil
  snps = []
  indels = []
  indels_map = {}

  puts "#{chr} #{chr_start} - #{chr_stop}"
  seq = sam.fetch_reference(chr,chr_start,chr_stop+1000)   
  sam.load_index
  
  upseq = seq.upcase
      
  
  
  als = []

  
  als = sam.fetch(chr, chr_start, chr_stop)  
  
  profile = []
  list = []
  start = nil
  alleles = {'A'=>0,'C'=>1,'G'=>2,'T'=>3}
  inv_alleles = {0=>'A',1=>'C',2=>'G',3=>'T'}
  
         
  als.each{|i|
    
    # puts "#{i.pos}"
           
               unless start
               start = i.pos  
               end
             
               if i.pos!=start
               
                 while start<i.pos 
                   del = []
                 
                   s = ''
                   ref = seq[start-chr_start]
                   print "#{start}\t#{ref}\t#{list.size}\t" if show
                   ref = ref.upcase
                 
                 
                  p = [0,0,0,0]
                  q = [0,0,0,0]
                  
                   list.each_with_index do|l,index|
                
                   
                     c = l.seq[start-l.pos]
                     cq = l.qual[start-l.pos]
                           
                    # a = seq[start-1..start-1-5]
                    # b =seq[start-l.pos..start-l.pos-5]
                    # puts "#{a} - #{b}"
                  
                     if c 
                      
                       case c 
                       when 'A'
                         p[0]+=1
                         q[0]+=cq-33 if cq 
                       when 'C'
                         p[1]+=1
                         q[1]+=cq-33 if cq 
                       when 'G'
                         p[2]+=1
                         q[2]+=cq-33 if cq 
                       when 'T'
                         p[3]+=1
                         q[3]+=cq-33 if cq 
                       end  
                      
                       s+=c                
                       
                       print "#{c}" if show
                   
                     else
                       del<<l
                     end
                   
                   
                   end
                 
                 
                  
                   pmax = p.index(p.max)
                   max = p[pmax]
                   p[pmax] = 0 if pmax
                   palt = p.index(p.max)
                   alt = p[palt]
                   dep = max+alt
                    max_q = q[pmax].to_f/max
                    alt_q = '0'
                    alt_q = q[palt].to_f/alt if alt > 0
                   
                     
                   if dep > 2 and ((indel = indels_map[start] and indel[:count]>1 )  or  (alt>0 and alt/dep.to_f > 0.1 and alt_q >10) or alleles[ref]!=pmax )
                     
                     
                         
                     text = "#{start}\t#{max}/#{alt.to_i}\t#{ref}\t#{s}"  
                     puts text  if var_show
                     sum = (max+alt).to_f
                     aalt = '-' 
                     
                     aalt = inv_alleles[palt] if alt!=0
                     if (alt>0 and alt/dep.to_f > 0.1)
                       c = 'a'
                     else
                       c = 'A'
                     end
                     
                     
                     if indel 
                      s = indel[:alleles].split('/')
                      ref = s[0]
                      aalt = s[1]
                      alt = indel[:count]
                      if indel[:type]=='ins'
                        c='+'
                      else
                        c='-'
                      end
                     end
                     snps << [chr,start,ref,inv_alleles[pmax],aalt,max,alt,format('%.2f',max_q),format('%.2f',alt_q),c]
                     
                     # snps << [chr,start,ref,inv_alleles[pmax],inv_alleles[palt],max,alt,max/sum,alt/sum]
                       
                   end
                   list-=del
                   if list.size==0
                   start = i.pos
                   else
                   start+=1
                   end

                 
                   puts if show
                 end
               
                 start = i.pos
               end
            
         
               
               seq_size = i.seq.size
               
               tseq = form(i.seq,i.cigar)
               tqual = form(i.qual,i.cigar)
               
               
               if (i.cigar.index('I') or i.cigar.index('D') ) 

                  
                  if indel_show  
                  puts "-------------------------INDEL " 
                  puts i.pos
                  puts i.cigar
                  puts i.seq
                  puts i.qual
                  # puts i.inspect

                  # :qname, :flag, :rname,:pos,:mapq,:cigar, :mrnm, :mpos, :isize, :seq, :qual, :tags, :al, :samstr
                  
                  puts seq[i.pos-chr_start..i.pos-chr_start+i.seq.size]
                  puts tseq[0]
                  puts tqual[0]
                  puts tseq[1]
                  end
                  
                            if tseq[1].size>0
                              for y in tseq[1]
                                if y[:type]=='ins'
                                  iref = '-'
                                  iseq = i.seq[y[:pos]..y[:pos]+y[:size]-1]
                                  y[:alleles] =  "#{iref}/#{iseq}"
                                else
                                  iref = seq[i.pos-chr_start+y[:pos]..i.pos-chr_start+y[:pos]+y[:size]-1]
                                  iseq = '-'
                                  y[:alleles] =  "#{iref}/#{iseq}"
                                end
                                y[:pos]+=i.pos
                                indels<<y
                                unless indels_map[y[:pos]]
                                    y[:count]=1
                                    y[:sm]=y[:alleles]
                                    indels_map[y[:pos]] = y
                                else
                                    indels_map[y[:pos]][:sm]+=",#{y[:alleles]}"
                                  
                                    indels_map[y[:pos]][:count] +=1
                                end

                              end
                            end
                  
                  
                end  
                  
                  
        
                    
              
              i.seq = tseq[0]
              i.qual = tqual[0].bytes.to_a
              
              
               if i.seq.size > seq_size/2
              
                   si = 0 
               
                   i.seq.size.times do |k|
                     # puts "#{i.seq[k]} #{seq[start-chr_start+k]}"
                     si+=1 if i.seq[k]==upseq[start-chr_start+k]
                   end
                   # puts "#{si} #{i.seq.size}"
                   if (si.to_f/i.seq.size)>=0.95
                     list << i 
                   else
                     if indel_show
                     puts "Drop with low similarity #{si.to_f/i.seq.size} #{i.cigar}"
                     puts seq[start-chr_start..start-chr_start+100]
                     puts i.seq
                     end
                   end
               end
                                   
               l = i 
         
    
           }
         
          
            if indel_show  
 
                for i in indels_map.keys.sort
                        puts indels_map[i].inspect
                end
           end
           # puts l.cigar
           # puts l.seq
           # puts snps.size
           return snps
  
end

.call_snv(params) ⇒ Object 



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# File 'lib/vardetect-vc/call_snv.rb', line 455

def self.call_snv params
  # ====================================================================================================
  # 1. VC calling 
  # ====================================================================================================
  core = 4
  core = params['core'].to_i if params['core'] # number of simultaneous processes
  sam_file =params['sam']
  ref_file =params['ref']
  vc_file =params['vc_out']
  p = {:sam=>sam_file,:ref=>ref_file,:output=>vc_file}

  # params[:start] = 95_658_000
  # params[:stop] = 95_659_000
  # call_variance params
  
  process_vc_multicore p,core
  # # params = {:sam=>sam_file,:ref=>ref_file,:output=>vc_all_file}
  # # process_vc_multicore params,core
end

.call_snv_range(params) ⇒ Object 



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# File 'lib/vardetect-vc/call_snv.rb', line 476

def self.call_snv_range params
  # ====================================================================================================
  # 1. VC calling 
  # ====================================================================================================
  core = 4
  core = params['core'].to_i if params['core'] # number of simultaneous processes
  sam_file =params['sam']
  ref_file =params['ref']
  vc_file =params['vc_out']
  p = {:sam=>sam_file,:ref=>ref_file,:output=>vc_file,:chr=>"chr#{params['chr']}",:start=>params['start'].to_i,:stop=>params['stop'].to_i,:debug=>'indel'}
  puts p.inspect
  
  call_variance p
  
end

.call_variance(p) ⇒ Object 



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# File 'lib/vardetect-vc/call_snv.rb', line 304

def self.call_variance p

  
  chr = p[:chr] 
  
  output = p[:output]
  testBAMFile = p[:sam]
  testReference = p[:ref]
  sam = Bio::DB::Sam.new({:bam=>testBAMFile, :fasta=>testReference})
  sam.open

  chr_start = p[:start]
  chr_stop  = p[:stop]
  snps = call_sam_snv sam,chr,chr_start,chr_stop, p[:debug]  
  
  sam.close
  f = File.open(output,'a')
  f.puts snps.collect{|j| j.join("\t")}
  f.close
end

.exec(args) ⇒ Object

command params options variance call



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# File 'lib/vardetect-vc.rb', line 26

def self.exec args
  params = parse_params args.join(' ')
  puts params.inspect
  
  cmd = params[:cmd]

  case cmd
    
  when 'snv'

    call_snv params
  
  when 'snv-batch'  
    
    path = '/Users/soup/Desktop/chula/data'
    path = params['path'] if params['path']
   
    working = params['exp']
    
    for i in params['samples'].split(',').compact
    
    sample_id = i
    
    
    ref_file = File.join(path,'ref','hg19.fa')
    sam_file = File.join(path,working,'bam',"#{sample_id}.remdup.uniqMap.TS.bam")
    vc_raw_file = File.join(path,working,'snv-vc',"#{sample_id}_vc_raw_snv.tsv")
    
    p = "snv -ref #{ref_file} -sam #{sam_file} -vc_out #{vc_raw_file} -core 16"
    
    p = parse_params(p)
    puts p.inspect
      call_snv p
    
    end
    
    
  when 'snv-range'

    call_snv_range params

  when 'prepare-st'

    call_prepare_st params

  when 'prepare-snp'

    call_prepare_snp params

  when 'prepare-vc'

    call_prepare_vc params

  when 'combine-all'

    call_combine_all params

  when 'analyse-combine'

    call_analyse_combine params
    
  end
  
end

.form(seq, cigar) ⇒ Object 



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# File 'lib/vardetect-vc/call_snv.rb', line 6

def self.form seq, cigar
  ix = cigar.split(/S|M|I|D/) 
  index = 0
  id = 0 
  str = ''
  st = 0
  indel = []
  # puts seq
  for i in ix
    index+=i.size
    cmd = cigar[index]
    # puts "#{cmd} #{i.to_i}"
    index+=1
    i = i.to_i
    case cmd
    when 'S'
      st = i 
      id += i 
    when 'I'
      indel<<{:pos=>id-st,:type=>'ins',:size=>i,:cigar=>cigar}
      id+=i
    when 'D'
      str+='N'*i
      indel<<{:pos=>id-st,:type=>'del',:size=>i,:cigar=>cigar}
    when 'M'
      str += seq[id..id+i-1] if seq[id..id+i-1]
      id+=i
    end
    # puts "Ref:#{seq}"
    # puts "Seq:#{str}"
    # puts "ID #{id}"
    # puts
  end
  return str,indel
end

.getidx(id) ⇒ Object 



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# File 'lib/vardetect-vc/call_combine.rb', line 279

def self.getidx id
  
  idx = {}
  %w{snp vc st pos ref vc_a1 vc_a vc_het vc_dep vc_alt vc_r snp_ann snp_a snp_het snp_gc snp_clus st_ref st_a2 st_qua st_dep st_alt st_pos}.each_with_index do |i,index|
    idx[i.to_sym] = index
  end
  return idx[id]
  
end

.hi ⇒ Object 



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# File 'lib/vardetect-vc.rb', line 20

def self.hi
  puts 'hello inside '
end

.inspect_reference(testReference) ⇒ Object 



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# File 'lib/vardetect-vc/call_snv.rb', line 327

def self.inspect_reference testReference
  
  # index reference 

  file = File.open(testReference,'r')
  map = {}
  size=0
  chr = nil
  while str=file.gets
    if str[0..0]=='>'
      if chr  
        puts "#{chr}\t#{size}"
        map[chr]=size  
      end 
      chr = str.strip.split[0][1..-1]
      size=0
    else
      size+=str.strip.size
    end
  end
  map[chr]=size
  puts map.inspect
  file.close
  genome = map
  # genome = {"chr1"=>249250621, "chr10"=>135534747, "chr11"=>135006516, "chr12"=>133851895, "chr13"=>115169878, "chr14"=>107349540, "chr15"=>102531392, "chr16"=>90354753, "chr17"=>81195210, "chr18"=>78077248, "chr19"=>59128983, "chr2"=>243199373, "chr20"=>63025520, "chr21"=>48129895, "chr22"=>51304566, "chr3"=>198022430, "chr4"=>191154276, "chr5"=>180915260, "chr6"=>171115067, "chr7"=>159138663, "chr8"=>146364022, "chr9"=>141213431, "chrX"=>155270560, "chrY"=>59373566}

  return genome
end

.inspect_reference_human(testReference) ⇒ Object 



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# File 'lib/vardetect-vc/call_snv.rb', line 356

def self.inspect_reference_human testReference
  
  # index reference 
  # 
  # file = File.open(testReference,'r')
  # map = {}
  # size=0
  # chr = nil
  # while str=file.gets
  #   if str[0..0]=='>'
  #     if chr  
  #       puts "#{chr}\t#{size}"
  #       map[chr]=size  
  #     end 
  #     chr = str[1..-1].strip
  #     size=0
  #   else
  #     size+=str.strip.size
  #   end
  # end
  # map[chr]=size
  # puts map.inspect
  # file.close

  genome = {"chr1"=>249250621, "chr10"=>135534747, "chr11"=>135006516, "chr12"=>133851895, "chr13"=>115169878, "chr14"=>107349540, "chr15"=>102531392, "chr16"=>90354753, "chr17"=>81195210, "chr18"=>78077248, "chr19"=>59128983, "chr2"=>243199373, "chr20"=>63025520, "chr21"=>48129895, "chr22"=>51304566, "chr3"=>198022430, "chr4"=>191154276, "chr5"=>180915260, "chr6"=>171115067, "chr7"=>159138663, "chr8"=>146364022, "chr9"=>141213431, "chrX"=>155270560, "chrY"=>59373566}

  return genome
end

.parse_params(params) ⇒ Object 



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# File 'lib/vardetect-vc/lib.rb', line 9

def self.parse_params params

  puts params 
  params = params.split
  cmd = params[0]
  tmp = {}
  ((params.size-1)/2).times do |i|
    key = params[1+i*2][1..-1]
    value = params[1+i*2+1]
    tmp[key]=value
  end
  tmp[:cmd]=cmd
  params = tmp 
end

.process_vc_multicore(params, core = 1, chr_filter = nil) ⇒ Object 



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# File 'lib/vardetect-vc/call_snv.rb', line 386

def self.process_vc_multicore  params, core=1,chr_filter=nil
  
  sim = core
   
  path = '/Users/soup/Desktop/vcqa'
  output = params[:output]
  
  testReference = params[:ref]

  genome = inspect_reference_human(testReference)

  if chr_filter # 1 as text
    
      tmp = {}
      chr = "chr#{chr_filter}"
      tmp[chr]=genome[chr]
      genome = tmp
  end

  puts genome.inspect


  # reset output
  f = File.open(output,'w')
  f.close

  a = []

  # job generator
  genome.each_pair do |chr,size|
    puts "#{chr}\t#{size}"
    m = 1000000
    n = size/m

    n.times do |i|
      params[:chr] = chr
      params[:start] = 1 + i * m
      params[:stop] = (i+1) * m
      a<<params.clone 
    end

    if size%m !=0
      params[:chr] = chr
      params[:start] = size - size% m
      params[:stop] = size
      a<<params.clone 
    end

  end

  sim = a.size if sim>a.size

  # starting first N processes
  sim.times do
    i = a.pop
    Process.fork{call_variance(i)}
  end
  # start one by one as the previous finish
  a.each do |i|
    Process.wait(0)
    Process.fork{call_variance(i)}
  end
  # wait for all to finish
  Process.waitall
  
end

.sampling(list) ⇒ Object 



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# File 'lib/vardetect-vc/call_combine.rb', line 290

def self.sampling list
  
  gcid = getidx :snp_gc
  depid = getidx :vc_dep
  vcrid = getidx :vc_r

  
  # =====================================================================
  # sampling gc score value from all data set
     gc_bin = []
     gc_range = 100
     gc_max = 1
     for i in list
       j = i[gcid].to_f
       k = (j * gc_range / gc_max).to_i 
       gc_bin[k]=0 unless gc_bin[k]
       gc_bin[k]+=1 
     end
     
   # =====================================================================
   # sampling dep score value from all data set
      d_bin = []
      d_range = 100
      d_max = 500
    
      for i in list
        j = i[depid].to_i
        k = (j * d_range / d_max).to_i 
        d_bin[k]=0 unless d_bin[k]
        d_bin[k]+=1 
      end

      # =====================================================================
      # sampling gc score value from all data set
        
      alt_bin = []
      alt_range = 100
      alt_max = 0.5
      dep_range = 100
      dep_max = 500
      
    
      for i in list
        
        j = i[vcrid].to_f
        d = i[depid].to_f
  
        k = (j * alt_range / alt_max).to_i 
        alt_bin[k]=0 unless alt_bin[k]
        alt_bin[k]+=1 
  
      end
      
      
      dot = []
      
      for i in list
        
        j = i[vcrid].to_f
        d = i[depid].to_f
        k = (j * alt_range / alt_max).to_i 
        k2 = (d * dep_range / dep_max).to_i 
        
        dot << "[#{d},#{j}]"
        
        
      end
      
      
      
      
      return {:gc=>gc_bin,:dep=>d_bin,:alt=>alt_bin,:dot=>dot}
     
end