Major change to terminology

  if (length(fname)>0) {

    while (getline < fname) {

      dups=$1;

      singdups=$2;

    }

  }

}

}

END{

  if (tot==0) tot=1;

  printf("Sequenced Read Pairs:  %'d\n Normal Paired: %'d (%0.2f%)\n Chimeric Paired: %'d (%0.2f%)\n Chimeric Ambiguous: %'d (%0.2f%)\n Unmapped: %'d (%0.2f%)\n", tot, norm, norm*100/tot, chim, chim*100/tot, coll, coll*100/tot, unm, unm*100/tot);

  if (length(singleend)==0) {

      printf("Read type: Paired End\n");

      printf("Sequenced Read Pairs:  %'d\n", tot);

      # in the future, 1 alignment - on one end / substantially overlapping in sum

      printf("No chimera found: %'d (%0.2f%)\n",  unm, unm*100/tot);

      printf(" One or both reads unmapped: %'d (%0.2f%)\n",  unm, unm*100/tot);

      # 1 alignment would go here and be in sum of "no chimera found"

      printf("2 alignments: %'d (%0.2f%)\n", norm+chim, (norm+chim)*100/tot);

      printf(" 2 alignments (A...B): %'d (%0.2f%)\n", norm, norm*100/tot);

      printf(" 2 alignments (A1….A2B; A1B2...B1A2): %'d (%0.2f%)\n", chim, chim*100/tot);

      printf("3 or more alignments: %'d (%0.2f%)\n", coll, coll*100/tot);

     if (ligation ~ /XXXX/) {

       printf("Ligation Motif Present: N/A\n");

     }

     else {

       printf("Ligation Motif Present: %'d (%0.2f%)\n", lig, lig*100/tot);

     }

     printf("Average insert size: %0.2f\n",insertsize/NR);

     alignable=norm+chim;

  printf(" Single Alignment: %'d (%0.2f%)\n Average insert size: %0.2f\nAlignable (Normal+Chimeric Paired): %'d (%0.2f%)\n",  singleton, singleton*100/tot, insertsize/NR, alignable, alignable*100/tot);

  uniq=alignable+singleton-dups;

     uniq=alignable-dups;

     if (alignable==0) alignable=1;

  printf("Unique Reads: %'d (%0.2f%, %0.2f%)\nDuplicates: %'d (%0.2f%, %0.2f%)\n", uniq, uniq*100/(alignable+singleton), uniq*100/tot, dups, dups*100/(alignable+singleton), dups*100/tot);

     printf("Total Unique: %'d (%0.2f%, %0.2f%)\nTotal Duplicates: %'d (%0.2f%, %0.2f%)\n", uniq, uniq*100/alignable, uniq*100/tot, dups, dups*100/alignable, dups*100/tot);

  }

  else {

      printf("Read type: Single End\n");

      printf("Sequenced Reads:  %'d\n", tot);

      # in the future, 1 alignment - on one end / substantially overlapping in sum

      printf("No chimera found: %'d (%0.2f%)\n",  unm+singleton, (unm+singleton)*100/tot);

      printf(" 0 alignments: %'d (%0.2f%)\n",  unm, unm*100/tot);

      printf(" 1 alignment: %'d (%0.2f%)\n",  singleton, singleton*100/tot);

      printf("2 alignments: %'d (%0.2f%)\n", chim, chim*100/tot);

      printf("3 or more alignments: %'d (%0.2f%)\n", coll, coll*100/tot);

     if (ligation ~ /XXXX/) {

       printf("Ligation Motif Present: N/A\n");

     }

     else {

       printf("Ligation Motif Present: %'d (%0.2f%)\n", lig, lig*100/tot);

     }

     singuniq=singleton-singdups;

     if (singleton==0) singleton=1;

     printf("1 alignment unique: %'d (%0.2f%, %0.2f%)\n", singuniq, singuniq*100/singleton, singuniq*100/tot);

     printf("1 alignment duplicates: %'d (%0.2f%, %0.2f%)\n", singdups, singdups*100/singleton, singdups*100/tot);

     #Library Complexity Estimate (1 alignment)*

     alignable=norm+chim;

     uniq=alignable-dups;

     if (alignable==0) alignable=1;

     printf("2 alignment unique: %'d (%0.2f%, %0.2f%)\n", uniq, uniq*100/alignable, uniq*100/tot);

     printf("2 alignment duplicates: %'d (%0.2f%, %0.2f%)\n", dups, dups*100/alignable, dups*100/tot);

     #Library Complexity Estimate (2 alignment)*

     printf("Total Unique: %'d (%0.2f%, %0.2f%)\n", uniq+singuniq, (uniq+singuniq)*100/(singleton+alignable), (uniq+singuniq)*100/tot);

     printf("Total Duplicates: %'d (%0.2f%, %0.2f%)\n", dups+singdups, (dups+singdups)*100/(singleton+alignable), (dups+singdups)*100/tot);

     #Library Complexity Estimate (1+2 above)*

  }

}