comparison libexec/consolidateResults.pl @ 10:f66f23fcc83a

Modified layout

8:2cee4ed50058

use Getopt::Long;
use Pod::Usage;

my $baseDir;
my $libDir;
#my $optDir;
#my $vcftDir;
BEGIN {
    my $thisDir=(File::Spec->splitpath($0))[1];
    $baseDir=File::Spec->catdir($thisDir,File::Spec->updir());
    $libDir=File::Spec->catdir($baseDir,'lib');
    #$optDir=File::Spec->catdir($baseDir,'opt');
    #$vcftDir=File::Spec->catdir($optDir,'vcftools','lib','perl5','site_perl');
}
use lib $libDir;
use Utils;
#use lib $vcftDir;
use Vcf;

if(getAbsPath($baseDir)) {
    errorX("Can't resolve path for strelka_workflow install directory: '$baseDir'");
}
#$optDir=File::Spec->catdir($baseDir,'opt');


my $scriptName=(File::Spec->splitpath($0))[2];
my $argCount=scalar(@ARGV);
my $cmdline=join(' ',$0,@ARGV);

GetOptions( "config=s" => \$configFile,
            "help|h" => \$help) or pod2usage(2);

pod2usage(2) if($help);
pod2usage(2) unless(defined($configFile));

#
# check fixed paths
#
#my $samtoolsBin = File::Spec->catfile($optDir,'samtools','samtools');
#checkFile($samtoolsBin,"samtools binary");


#
# read config and validate values
#
checkFile($configFile,"configuration ini");

    }

    return unless(scalar(@bamList));

    my $headerFH = File::Temp->new();
    my $getHeaderCmd = "bash -c '$samtoolsBin view -H ".$bamList[0]." > $headerFH'";
    executeCmd($getHeaderCmd);

    my $allFile = File::Spec->catfile($reDir,$fileName . $itag);
    my $cmd="$samtoolsBin merge -h $headerFH $allFile ". join(" ",@bamList);
    executeCmd($cmd);

    my $allFileFinished = File::Spec->catfile($reDir,$fileName);
    checkMove($allFile,$allFileFinished);

    my $indexCmd="$samtoolsBin index $allFileFinished";
    executeCmd($indexCmd);

    # for now don't remove all the bin realignments...
    # unlink(@bamList);
}

10:f66f23fcc83a

use Getopt::Long;
use Pod::Usage;

my $baseDir;
my $libDir;
BEGIN {
    my $thisDir=(File::Spec->splitpath($0))[1];
    $baseDir=File::Spec->catdir($thisDir,File::Spec->updir());
    $libDir=File::Spec->catdir($baseDir,'lib');
}
use lib $libDir;
use Utils;
use Vcf;

if(getAbsPath($baseDir)) {
    errorX("Can't resolve path for strelka_workflow install directory: '$baseDir'");
}


my $scriptName=(File::Spec->splitpath($0))[2];
my $argCount=scalar(@ARGV);
my $cmdline=join(' ',$0,@ARGV);

GetOptions( "config=s" => \$configFile,
            "help|h" => \$help) or pod2usage(2);

pod2usage(2) if($help);
pod2usage(2) unless(defined($configFile));

#
# read config and validate values
#
checkFile($configFile,"configuration ini");

    }

    return unless(scalar(@bamList));

    my $headerFH = File::Temp->new();
    my $getHeaderCmd = "bash -c 'samtools view -H ".$bamList[0]." > $headerFH'";
    executeCmd($getHeaderCmd);

    my $allFile = File::Spec->catfile($reDir,$fileName . $itag);
    my $cmd="samtools merge -h $headerFH $allFile ". join(" ",@bamList);
    executeCmd($cmd);

    my $allFileFinished = File::Spec->catfile($reDir,$fileName);
    checkMove($allFile,$allFileFinished);

    my $indexCmd="samtools index $allFileFinished";
    executeCmd($indexCmd);

    # for now don't remove all the bin realignments...
    # unlink(@bamList);
}