adding in addstats script for mega

#!/usr/bin/awk -f

##########

#The MIT License (MIT)

#

# Copyright (c) 2015 Aiden Lab

#

# Permission is hereby granted, free of charge, to any person obtaining a copy

# of this software and associated documentation files (the "Software"), to deal

# in the Software without restriction, including without limitation the rights

# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

# copies of the Software, and to permit persons to whom the Software is

# furnished to do so, subject to the following conditions:

#

# The above copyright notice and this permission notice shall be included in

# all copies or substantial portions of the Software.

#

#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

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#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN

#  THE SOFTWARE.

##########

# Helper script for taking in multiple inter.txt and producing sums

# Juicer version 1.5

$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);

}