Mega map stats script

$1=="Sequenced"{

gsub(/,/,"",$4);

 total=total+$4;

}

$1=="Unmapped:"{

gsub(/,/,"",$2);

 unmapped=unmapped+$2

}

$1=="Normal"{

gsub(/,/,"",$3);

 regular=regular+$3}

$1=="Chimeric" && $2=="Paired:"{

gsub(/,/,"",$3);

 normal=normal+$3}

$2=="Ambiguous:"{

gsub(/,/,"",$3);

 abnorm=abnorm+$3}

$1=="Alignable"{

gsub(/,/,"",$4);

 alignable=alignable+$4}

$1=="Unique" {

gsub(/,/,"",$3);

 dedup=dedup+$3}

$1=="PCR"{

gsub(/,/,"",$3);

 dups=dups+$3}

$1=="Optical"{

gsub(/,/,"",$3);

 optdups=optdups+$3}

END{

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

 printf(" %s %'d (%0.2f%)\n", "Normal Paired:", regular, regular*100/total);

 printf(" %s %'d (%0.2f%)\n", "Chimeric Paired:", normal, normal*100/total);

 printf(" %s %'d (%0.2f%)\n", "Chimeric Ambiguous:", abnorm, abnorm*100/total);

 printf(" %s %'d (%0.2f%)\n", "Unmapped:", unmapped, unmapped*100/total);

 printf(" %s %'d (%0.2f%)\n", "Alignable (Normal+Chimeric Paired):", alignable, alignable*100/total);

 printf("%s %'d\n", "Unique Reads:", dedup);

 printf("%s %'d\n", "PCR Duplicates:", dups);

  printf("%s %'d\n", "Optical Duplicates:", optdups);

}