text: 
  chroms = ['chr{}'.format(x) for x in range(1,23)] + ['chrX']
  
  for c in chroms:
      duitama_chrom_pos = []
      with open("data/temp/duitama_haplotypes/{}.real_refhap.phase".format(c),'r') as duitama_file:
          for line in duitama_file:
              el = line.strip().split()
              pos = int(el[0])
              duitama_chrom_pos.append((c, pos))
  
      NA12878_chrom_pos = []
      with open("data/NA12878_hg18_VCFs/{}.vcf".format(c),'r') as NA12878_vcf:
          for line in NA12878_vcf:
              # header lines
              if line[0] == '#':
                  continue
  
              el = line.strip().split('\t')
              chrom = el[0] # add chr label
              pos = int(el[1])
  
              NA12878_chrom_pos.append((chrom,pos))
  
      print("checking that indices in Duitama haplotype with {} elements matches indices in NA12878 haplotype with {} elements...".format(len(duitama_chrom_pos), len(NA12878_chrom_pos)))
      assert(duitama_chrom_pos == NA12878_chrom_pos)
      print("...PASSED")
  