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1 #!/usr/bin/perl -s
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2 #Merge Softsearch results by chrom
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3 if(!$ARGV[0]){die "Usage: <Sample.1.vcf>\n";}
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4 my ($sample,$cmd);
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5
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6 #Get basename
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7 $sample="$ARGV[0]";
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8 $sample=~s/.[0-9(+)].out.vcf//;
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9 $sample=~s/.[0-9(+)].pe.vcf//;
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10
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11 my $outfile=$sample;
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12 $outfile.="out.vcf";
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13 if( -e $outfile ){unlink($outfile)}
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14 $cmd="ls $sample\*vcf";
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15 my @samples=`$cmd`;
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16 print "there are " .scalar(@samples)." samples\n";
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17
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18 open (OUT,">$outfile");
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19 my $i=1;
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20 my $tmp=@samples[$i];
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21 open(TMP,"$tmp");
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22 while (<TMP>){
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23 print OUT if ($_=~/^#/);
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24 }
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25
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26 open (OUT,">>$outfile");
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27 my $chr;
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28 for (my $i=0;$i<@samples;$i++){
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29 my $tmp=@samples[$i];
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30 open(TMP,"$tmp");
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31 while (<TMP>){
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32 unless (($_=~/^chrGL/)||($_=~/^#/)){print OUT $_;}
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33 }
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34 print "Done with $tmp";
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35 unlink($tmp);
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36 system("rm $tmp");
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37 close TMP;
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38 }
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39 close OUT;
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