--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/strelka2/libexec/consolidateResults.pl	Thu Sep 25 11:59:08 2014 -0400
@@ -0,0 +1,276 @@
+#!/usr/bin/env perl
+
+=head1 LICENSE
+
+Strelka Workflow Software
+Copyright (c) 2009-2013 Illumina, Inc.
+
+This software is provided under the terms and conditions of the
+Illumina Open Source Software License 1.
+
+You should have received a copy of the Illumina Open Source
+Software License 1 along with this program. If not, see
+<https://github.com/downloads/sequencing/licenses/>.
+
+=head1 SYNOPSIS
+
+consolidateSomaticVariants.pl [options] | --help
+
+=head2 SUMMARY
+
+Aggregate final results from all chromosomes
+
+=cut
+
+use warnings FATAL => 'all';
+use strict;
+
+use Carp;
+$SIG{__DIE__} = \&Carp::confess;
+
+use File::Spec;
+use File::Temp;
+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);
+
+
+my $configFile;
+my $help;
+
+GetOptions( "config=s" => \$configFile,
+            "help|h" => \$help) or pod2usage(2);
+
+pod2usage(2) if($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");
+my $config  = parseConfigIni($configFile);
+
+
+for (qw(outDir chromOrder)) {
+    errorX("Undefined configuration option: '$_'") unless(defined($config->{derived}{$_}));
+}
+for (qw(isWriteRealignedBam binSize)) {
+    errorX("Undefined configuration option: '$_'") unless(defined($config->{user}{$_}));
+}
+
+my $userconfig = $config->{user};
+
+my @chromOrder = split(/\t/,$config->{derived}{chromOrder});
+for my $chrom (@chromOrder) {
+    my $chromSizeKey = "chrom_" . $chrom . "_size";
+    errorX("Undefined configuration option: '$_'") unless(defined($chromSizeKey));
+}
+
+my $outDir = $config->{derived}{outDir};
+checkDir($outDir,"output");
+
+
+my $isWriteRealignedBam = $userconfig->{isWriteRealignedBam};
+
+for my $chrom (@chromOrder) {
+    my $chromDir = File::Spec->catdir($outDir,'chromosomes',$chrom);
+    checkDir($chromDir,"input chromosome");
+
+    next unless($isWriteRealignedBam);
+    my $chromSizeKey = "chrom_" . $chrom . "_size";
+    my $binList = getBinList($config->{derived}{$chromSizeKey},$userconfig->{binSize});
+    for my $binId (@$binList) {
+        my $dir = File::Spec->catdir($chromDir,'bins',$binId);
+        checkDir($dir,"input bin");
+    }
+}
+
+
+
+# suffix used for large result file intermediates:
+my $itag = ".incomplete";
+
+
+#
+# concatenate vcfs:
+#
+sub concatenateVcfs($) {
+    my $fileName = shift;
+
+    my $is_first = 1;
+
+    my $allFileName = "all." . $fileName;
+    my $allFile = File::Spec->catfile($outDir,'results',$allFileName . $itag);
+    open(my $aFH,'>',"$allFile")
+          || errorX("Failed to open file: '$allFile'");
+
+    # loop over all chroms once to create the header, and one more time for all the data:
+    my $headervcf;
+    for my $chrom (@chromOrder) {
+        my $chromDir = File::Spec->catdir($outDir,'chromosomes',$chrom);
+        my $iFile = File::Spec->catfile($chromDir,$fileName);
+        checkFile($iFile);
+
+        my $depthKey="maxDepth_${chrom}";
+
+        if($is_first) {
+            open(my $iFH,'<',"$iFile")
+                || errorX("Failed to open file: '$iFile'");
+            $headervcf = Vcf->new(fh=>$iFH);
+            $headervcf->parse_header();
+            $headervcf->remove_header_line(key=>"cmdline");
+            $headervcf->add_header_line({key=>"cmdline",value=>$cmdline});
+            $headervcf->remove_header_line(key=>"$depthKey");
+            close($iFH);
+            $is_first=0;
+        }
+
+        {
+            open(my $iFH,'<',"$iFile")
+                || errorX("Failed to open file: '$iFile'");
+            my $vcf = Vcf->new(fh=>$iFH);
+            $vcf->parse_header();
+            for my $line (@{$vcf->get_header_line(key=>"$depthKey")}) {
+                # $line seems to be returned as a length 1 array ref to a hash --  ??!?!??!!
+                $headervcf->add_header_line($line->[0]);
+            }
+            $vcf->close();
+            close($iFH);
+         }
+    }
+    print $aFH $headervcf->format_header();
+    $headervcf->close();
+
+    for my $chrom (@chromOrder) {
+        my $chromDir = File::Spec->catdir($outDir,'chromosomes',$chrom);
+        my $iFile = File::Spec->catfile($chromDir,$fileName);
+
+        open(my $iFH,'<',"$iFile")
+            || errorX("Failed to open file: '$iFile'");
+
+        my $vcf = Vcf->new(fh=>$iFH);
+        $vcf->parse_header();
+        print $aFH $_ while(<$iFH>);
+    }
+
+    close($aFH);
+
+    # make a second set of files with only the passed variants:
+    my $passedFileName = "passed." . $fileName;
+    my $passedFile = File::Spec->catfile($outDir,'results',$passedFileName . $itag);
+    open(my $pFH,'>',"$passedFile")
+          || errorX("Failed to open file: '$passedFile'");
+
+    open(my $arFH,'<',"$allFile")
+          || errorX("Failed to open file: '$allFile'");
+
+    while(<$arFH>) {
+        chomp;
+        unless(/^#/) {
+            my @F = split(/\t/);
+            next if((scalar(@F)>=7) && ($F[6] ne "PASS"));
+        }
+        print $pFH "$_\n";
+    }
+
+    close($arFH);
+    close($pFH);
+
+    my $allFileFinished = File::Spec->catfile($outDir,'results',$allFileName);
+    checkMove($allFile,$allFileFinished);
+
+    my $passedFileFinished = File::Spec->catfile($outDir,'results',$passedFileName);
+    checkMove($passedFile,$passedFileFinished);
+}
+
+concatenateVcfs("somatic.snvs.vcf");
+concatenateVcfs("somatic.indels.vcf");
+
+
+my $bamSuffix = ".realigned.bam";
+
+sub consolidateBam($) {
+    my $label = shift;
+
+    my $fileName = $label . $bamSuffix;
+
+    my $reDir = File::Spec->catdir($outDir,'realigned');
+    checkMakeDir($reDir);
+
+    my @bamList;
+    for my $chrom (@chromOrder) {
+        my $chromDir = File::Spec->catdir($outDir,'chromosomes',$chrom);
+
+        my $chromSizeKey = "chrom_" . $chrom . "_size";
+        my $binList = getBinList($config->{derived}{$chromSizeKey},$userconfig->{binSize});
+        for my $binId (@$binList) {
+            my $binDir = File::Spec->catdir($chromDir,'bins',$binId);
+            my $rbamFile = File::Spec->catfile($binDir,$fileName);
+            checkFile($rbamFile,"bin realigned bam file");
+
+            push @bamList,$rbamFile;
+        }
+    }
+
+    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);
+}
+
+if($isWriteRealignedBam) {
+    consolidateBam("normal");
+    consolidateBam("tumor");
+}
+
+
+1;
+
+__END__
+