update add stats file

# Juicer version 2.0

$1=="Sequenced"{

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

  tot=tot+$4;

 total=total+$4;

}

$1=="Unmapped:"{

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

 unm=unm+$2

 unmapped=unmapped+$2

}

$1=="Normal"{

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

  norm=norm+$3}

 regular=regular+$3}

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

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

  chim=chim+$3}

$1=="MAPQ" && $2=="0:"{

 normal=normal+$3}

$2=="Ambiguous:"{

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

  mapq0=mapq0+$3}

$1=="Collisions:"{

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

  coll=coll+$2}

$3=="Collisions:"{

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

  lowc=lowc+$4}

$1=="Ligation" {

 abnorm=abnorm+$3}

$1=="Alignable"{

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

  lig=lig+$4}

 alignable=alignable+$4}

$1=="Unique" {

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

 dedup=dedup+$3}

$1=="PCR"{

$1=="Duplicates:"{

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

 dups=dups+$3}

$1=="Optical"{

$1=="Ligation"{

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

 ligs=ligs+$4}

$1=="Single"{

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

  optdups=optdups+$3}

 single=single+$3}

$1=="Average"{

 avg_insert=avg_insert+$4;

}

END{

  printf("Sequenced Read Pairs:  %'d\n Normal Paired: %'d (%0.2f%)\n Chimeric Paired: %'d (%0.2f%)\n Collisions: %'d (%0.2f%)\n Low MAPQ Collisions: %'d (%0.2f%)\n Unmapped: %'d (%0.2f%)\n MAPQ 0: %'d (%0.2f%)\n Ligation Motif Present: %'d (%0.2f%)\nAlignable (Normal+Chimeric Paired): %'d (%0.2f%)\n Unique Reads: %'d\n PCR Duplicates: %'d\n Optical Duplicates: %'d\n", tot, norm, norm*100/tot, chim, chim*100/tot, coll, coll*100/tot, lowc, lowc*100/tot, unm, unm*100/tot, mapq0, mapq0*100/tot, lig, lig*100/tot, norm+chim, (norm+chim)*100/tot, dedup, dups, optdups );

 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", "Ligation Motif Present:", ligs, ligs*100/total);

 printf(" %s %'d (%0.2f%)\n", "Single Alignment:", single, single*100/total);

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

 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", "Duplicates:", dups);

}