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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 use warnings;
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5 use Getopt::Long;
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6
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7 use Bio::Seq::GenomeID qw(generate_id);
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8
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9 my ($outFile, $inFile, $type, $index, $hg);
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10 my ($noise, $baq, $sex, $ucn, $ref, $name);
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11
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12 GetOptions("o=s"=> \$outFile,
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13 "n=f"=>\$noise,
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14 "hg=s"=> \$hg,
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15 "b=i"=> \$baq,
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16 "s=s"=> \$sex,
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17 "u=s"=> \$ucn,
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18 "r=s"=> \$ref,
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19 "type=s"=> \$type,
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20 "file=s"=> \$inFile,
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21 "sN=s"=> \$name,
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22 );
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23 $ucn = ($ucn eq "true")? 1:0; $sex = ($sex eq "true")?1:0; $ref = ($ref eq "true")?1:0;
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24
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25 my %obj;
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26 $obj{'type'} = $type; $obj{'file'} = $inFile;
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27 $obj{'ucn'} = $ucn; $obj{'sex'} = $sex; $obj{'ref'} = $ref;
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28 $obj{'noise'} = $noise; $obj{'baq'} = $baq;
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29
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30 if($type eq "tbi"){
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31 `tabix -p vcf $inFile`;
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32 }
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33
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34
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35 if($hg ne "none"){
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36 $obj{'hg'} = $hg;
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37 }
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38
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39 if( defined $name ){
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40 $obj{'sampleName'} = $name;
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41 }
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42
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43 my $genomeID = generate_id(%obj);
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44 open(my $fh, '>', $outFile);
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45 print $fh $genomeID;
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46 close $fh;
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