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1 use strict;
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2 use warnings;
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3 use File::Basename;
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4 use Cwd;
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5 use File::Path qw(make_path remove_tree);
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6 die qq(
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7 Bad numbr of inputs
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8
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9 ) if(!@ARGV);
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10
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11 my $options ="";
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12 my $normal="";
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13 my $tumor="";
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14 my $output="";
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15
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16
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17 foreach my $input (@ARGV)
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18 {
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19 my @tmp = split "::", $input;
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20 if($tmp[0] eq "NORMAL")
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21 {
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22 $normal = $tmp[1];
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23 }
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24 elsif($tmp[0] eq "TUMOR")
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25 {
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26 $tumor = $tmp[1];
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27 }
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28 elsif($tmp[0] eq "OUTPUT")
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29 {
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30 $output = $tmp[1];
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31 }
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32 elsif($tmp[0] eq "OPTION")
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33 {
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34 $options = "$options ${tmp[1]}";
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35 }
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36
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37 else
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38 {
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39 die("Unknown Input: $input\n");
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40 }
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41 }
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42
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43
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44 my $working_dir = cwd();
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45
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46 system ("ln -s $normal $working_dir/normal.bam");
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47 system ("samtools index $working_dir/normal.bam");
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48
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49 system ("ln -s $tumor $working_dir/tumor.bam");
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50 system ("samtools index $working_dir/tumor.bam");
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51
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52 system ("bam-somaticsniper $options $working_dir/tumor.bam $working_dir/normal.bam $output");
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53
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54
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