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comparison libexec/consolidateResults.pl @ 9:0e8e6011082b

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Strelka Workflow 0.0.2
author mini
date Fri, 26 Sep 2014 15:51:35 +0200
parents 87568e5a7d4f
children
comparison
equal deleted inserted replaced
8:2cee4ed50058 9:0e8e6011082b
33 use Getopt::Long; 33 use Getopt::Long;
34 use Pod::Usage; 34 use Pod::Usage;
35 35
36 my $baseDir; 36 my $baseDir;
37 my $libDir; 37 my $libDir;
38 #my $optDir;
39 #my $vcftDir;
40 BEGIN { 38 BEGIN {
41 my $thisDir=(File::Spec->splitpath($0))[1]; 39 my $thisDir=(File::Spec->splitpath($0))[1];
42 $baseDir=File::Spec->catdir($thisDir,File::Spec->updir()); 40 $baseDir=File::Spec->catdir($thisDir,File::Spec->updir());
43 $libDir=File::Spec->catdir($baseDir,'lib'); 41 $libDir=File::Spec->catdir($baseDir,'lib');
44 #$optDir=File::Spec->catdir($baseDir,'opt');
45 #$vcftDir=File::Spec->catdir($optDir,'vcftools','lib','perl5','site_perl');
46 } 42 }
47 use lib $libDir; 43 use lib $libDir;
48 use Utils; 44 use Utils;
49 #use lib $vcftDir;
50 use Vcf; 45 use Vcf;
51 46
52 if(getAbsPath($baseDir)) { 47 if(getAbsPath($baseDir)) {
53 errorX("Can't resolve path for strelka_workflow install directory: '$baseDir'"); 48 errorX("Can't resolve path for strelka_workflow install directory: '$baseDir'");
54 } 49 }
55 #$optDir=File::Spec->catdir($baseDir,'opt');
56 50
57 51
58 my $scriptName=(File::Spec->splitpath($0))[2]; 52 my $scriptName=(File::Spec->splitpath($0))[2];
59 my $argCount=scalar(@ARGV); 53 my $argCount=scalar(@ARGV);
60 my $cmdline=join(' ',$0,@ARGV); 54 my $cmdline=join(' ',$0,@ARGV);
66 GetOptions( "config=s" => \$configFile, 60 GetOptions( "config=s" => \$configFile,
67 "help|h" => \$help) or pod2usage(2); 61 "help|h" => \$help) or pod2usage(2);
68 62
69 pod2usage(2) if($help); 63 pod2usage(2) if($help);
70 pod2usage(2) unless(defined($configFile)); 64 pod2usage(2) unless(defined($configFile));
71
72 #
73 # check fixed paths
74 #
75 #my $samtoolsBin = File::Spec->catfile($optDir,'samtools','samtools');
76 #checkFile($samtoolsBin,"samtools binary");
77
78 65
79 # 66 #
80 # read config and validate values 67 # read config and validate values
81 # 68 #
82 checkFile($configFile,"configuration ini"); 69 checkFile($configFile,"configuration ini");
245 } 232 }
246 233
247 return unless(scalar(@bamList)); 234 return unless(scalar(@bamList));
248 235
249 my $headerFH = File::Temp->new(); 236 my $headerFH = File::Temp->new();
250 my $getHeaderCmd = "bash -c '$samtoolsBin view -H ".$bamList[0]." > $headerFH'"; 237 my $getHeaderCmd = "bash -c 'samtools view -H ".$bamList[0]." > $headerFH'";
251 executeCmd($getHeaderCmd); 238 executeCmd($getHeaderCmd);
252 239
253 my $allFile = File::Spec->catfile($reDir,$fileName . $itag); 240 my $allFile = File::Spec->catfile($reDir,$fileName . $itag);
254 my $cmd="$samtoolsBin merge -h $headerFH $allFile ". join(" ",@bamList); 241 my $cmd="samtools merge -h $headerFH $allFile ". join(" ",@bamList);
255 executeCmd($cmd); 242 executeCmd($cmd);
256 243
257 my $allFileFinished = File::Spec->catfile($reDir,$fileName); 244 my $allFileFinished = File::Spec->catfile($reDir,$fileName);
258 checkMove($allFile,$allFileFinished); 245 checkMove($allFile,$allFileFinished);
259 246
260 my $indexCmd="$samtoolsBin index $allFileFinished"; 247 my $indexCmd="samtools index $allFileFinished";
261 executeCmd($indexCmd); 248 executeCmd($indexCmd);
262 249
263 # for now don't remove all the bin realignments... 250 # for now don't remove all the bin realignments...
264 # unlink(@bamList); 251 # unlink(@bamList);
265 } 252 }