Case 1:
genome: GAAACACTGACGTTCTTACTGACGCAGAAGAAAAC
         2001112121310220312121331220220001
        ^                                         (^ genomeIndex = 777)
read: A55200111212131022031212133121322000	  (tag: unknown_0001:8:1:1044:2657#0/1)
       N===========================T======        (35 bp)
       NGAAACACTGACGTTCTTACTGACGCAGTAGAAAA
       0        0         0         012345        (35 bp)
       NNN==ACAGNNNNNNTCCNNNNNNCGTACGAG==A	  
       NNNAAACAGNNNNNNTCCNNNNNNCGTACGAGAAA
      ANNAAACACTGACGTTCTTACTGACGCAGCGGAAAA
                                   ^
//Case 2:
      TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCT	  (gs)
       1010231022033031002022120311211332         (csgs)
      31010231022033031002022120311211355A	  (read)
      TGGTTCGTTCTTATTACCCTTCTGAATGTCACGTNA	  (read)
      TACCAAGCAAGAATAATGGGAAGACTTACAGTGCN	  (phiX.cs.sam)
      ==================================N         (phiX.sam)
      TACCAAGCAAGAATAATGGGAAGACTTACAGTGCN         (phiX.sam)
      ATGGTTCGTTCTTATTACCCTTCTGAATGTCACGN	  (phiX.sam comp)
      ^						  (genomeMatchPosition)

      ACCAAGCAAGAATAATGGGAAGACTTACAGTGCAN

      NCGTGACATTCAGAAGGGTAATAAGAACGAACCAT         (phiX.fastq)
