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1 #!/usr/bin/perl
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2
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3 use strict;
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4 my %read1;
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5 my %read2;
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6 my %qual1;
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7 my %qual2;
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8
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9 while (my $line=<STDIN>) {
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10 chomp();
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11 my ($name, $flag, $chr1, $pos1, $mq, $cigar, $chr2, $pos2, $dist, $seq, $quals, $stuff)=split(/\s+/, $line);
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12 if($flag & 16) { #reverse-complement it
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13 $seq=reverse($seq);
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14 $seq=~tr/ACGT/TGCA/;
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15 $quals=reverse($quals);
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16 }
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17 if($flag & 64) { #first in pair
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18 $read1{$name}=$seq;
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19 $qual1{$name}=$quals;
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20 }
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21 else {
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22 $read2{$name}=$seq;
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23 $qual2{$name}=$quals;
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24 }
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25 }
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26
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27 open(FQ1, ">$ARGV[0]") or die "Can't open $ARGV[0]";
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28 open(FQ2, ">$ARGV[1]") or die "Can't open $ARGV[1]";
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29 open(FQ3, ">$ARGV[2]") or die "Can't open $ARGV[2]";
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30
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31 foreach my $key(keys %read1) {
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32
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33 if(exists $read2{$key}) {
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34 print FQ1 "\@$key\n$read1{$key}\n+\n$qual1{$key}\n";
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35 print FQ2 "\@$key\n$read2{$key}\n+\n$qual2{$key}\n";
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36 }
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37 else {
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38 print FQ3 "\@$key\n$read1{$key}\n+\n$qual1{$key}\n";
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39 }
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40 }
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41 foreach my $key(keys %read2) {
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42
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43 if(!(exists $read1{$key})) {
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44 print FQ3 "\@$key\n$read2{$key}\n+\n$qual2{$key}\n";
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45 }
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46 }
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47 close(FQ1);
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48 close(FQ2);
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49 close(FQ3);
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50
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51
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52
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53 |
