--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/strelka2/libexec/filterSomaticVariants.pl	Thu Sep 25 11:59:08 2014 -0400
@@ -0,0 +1,435 @@
+#!/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
+
+filterSomaticVariants.pl [options] | --help
+
+=head2 SUMMARY
+
+Aggregate and filter the variant caller results by chromosome
+
+=cut
+
+use warnings FATAL => 'all';
+use strict;
+
+use Carp;
+$SIG{__DIE__} = \&Carp::confess;
+
+use File::Spec;
+use Getopt::Long;
+use Pod::Usage;
+
+my $baseDir;
+my $libDir;
+#my $vcftDir;
+BEGIN {
+    my $thisDir=(File::Spec->splitpath($0))[1];
+    $baseDir=File::Spec->catdir($thisDir,File::Spec->updir());
+    $libDir=File::Spec->catdir($baseDir,'lib');
+    #my $optDir=File::Spec->catdir($baseDir,'opt');
+    #$vcftDir=File::Spec->catdir($optDir,'vcftools','lib','perl5','site_perl');
+}
+use lib $libDir;
+use Utils;
+#use lib $vcftDir;
+#use Vcf;
+
+
+my $scriptName=(File::Spec->splitpath($0))[2];
+my $argCount=scalar(@ARGV);
+my $cmdline = join(' ',$0,@ARGV);
+
+
+my ($chrom, $configFile);
+my $help;
+
+GetOptions( "chrom=s" => \$chrom,
+            "config=s" => \$configFile,
+            "help|h" => \$help) or pod2usage(2);
+
+pod2usage(2) if($help);
+pod2usage(2) unless(defined($chrom));
+pod2usage(2) unless(defined($configFile));
+
+
+
+#
+# read config and validate values
+#
+checkFile($configFile,"configuration ini");
+my $config  = parseConfigIni($configFile);
+
+my $chromSizeKey = "chrom_" . $chrom . "_size";
+my $chromKnownSizeKey = "chrom_" . $chrom . "_knownSize";
+
+for (("outDir", $chromSizeKey, $chromKnownSizeKey)) {
+    errorX("Undefined configuration option: '$_'") unless(defined($config->{derived}{$_}));
+}
+for (qw(binSize ssnvQuality_LowerBound sindelQuality_LowerBound
+        isSkipDepthFilters depthFilterMultiple
+        snvMaxFilteredBasecallFrac snvMaxSpanningDeletionFrac
+        indelMaxRefRepeat indelMaxWindowFilteredBasecallFrac
+        indelMaxIntHpolLength)) {
+    errorX("Undefined configuration option: '$_'") unless(defined($config->{user}{$_}));
+}
+
+my $outDir = $config->{derived}{outDir};
+my $chromDir = File::Spec->catdir($outDir,'chromosomes',$chrom);
+checkDir($outDir,"output");
+checkDir($chromDir,"output chromosome");
+
+my $userconfig = $config->{user};
+
+my $binList = getBinList($config->{derived}{$chromSizeKey},$userconfig->{binSize});
+for my $binId (@$binList) {
+    my $dir = File::Spec->catdir($chromDir,'bins',$binId);
+    checkDir($dir,"input bin");
+}
+
+#
+# parameters from user config file:
+#
+
+# minimum passed ssnv_nt Q-score:
+my $minQSSNT=$userconfig->{ssnvQuality_LowerBound};
+# minimum passed sindel_nt Q-score:
+my $minQSINT=$userconfig->{sindelQuality_LowerBound};
+
+#
+# filtration parameters from user config file:
+#
+
+# skip depth filters for targeted resequencing:
+my $isUseDepthFilter=(! $userconfig->{isSkipDepthFilters});
+# multiple of the normal mean coverage to filter snvs and indels
+my $depthFilterMultiple=$userconfig->{depthFilterMultiple};
+# max filtered basecall fraction for any sample
+my $snvMaxFilteredBasecallFrac=$userconfig->{snvMaxFilteredBasecallFrac};
+# max snv spanning-deletion fraction for any sample
+my $snvMaxSpanningDeletionFrac=$userconfig->{snvMaxSpanningDeletionFrac};
+# max indel reference repeat length
+my $indelMaxRefRepeat=$userconfig->{indelMaxRefRepeat};
+# max indel window filter fraction
+my $indelMaxWindowFilteredBasecallFrac=$userconfig->{indelMaxWindowFilteredBasecallFrac};
+# max indel interupted hompolymer length:
+my $indelMaxIntHpolLength=$userconfig->{indelMaxIntHpolLength};
+
+
+# first we want the normal sample mean chromosome depth:
+#
+my $filterCoverage;
+if($isUseDepthFilter) {
+    my $totalCoverage = 0;
+    for my $binId (@$binList) {
+        my $sFile = File::Spec->catfile($chromDir,'bins',$binId,'strelka.stats');
+        checkFile($sFile,"strelka bin stats");
+        open(my $sFH, '<', $sFile)
+          || errorX("Can't open file: '$sFile' $!");
+
+        my $is_found=0;
+        while(<$sFH>) {
+            next unless(/^NORMAL_NO_REF_N_COVERAGE\s/);
+            my $is_bad = 0;
+            if(not /sample_size:\s*(\d+)\s+/) { $is_bad=1; }
+            my $ss=$1;
+            # leave the regex for mean fairly loose to pick up scientific notation, etc..
+            if(not /mean:\s*(\d[^\s]*|nan)\s+/) { $is_bad=1; }
+            my $mean=$1;
+            errorX("Unexpected format in file: '$sFile'") if($is_bad);
+
+            my $coverage = ( $ss==0 ? 0 : int($ss*$mean) );
+
+            $totalCoverage += $coverage;
+            $is_found=1;
+            last;
+        }
+        close($sFH);
+        errorX("Unexpected format in file: '$sFile'") unless($is_found);
+    }
+
+    my $chromKnownSize = $config->{derived}{$chromKnownSizeKey};
+    my $normalMeanCoverage = ($totalCoverage/$chromKnownSize);
+    $filterCoverage = $normalMeanCoverage*$depthFilterMultiple;
+}
+
+
+# add filter description to vcf header unless it already exists
+# return 1 if filter id already exists, client can decide if this is an error
+#
+sub add_vcf_filter($$$) {
+    my ($vcf,$id,$desc) = @_;
+    return 1 if(scalar(@{$vcf->get_header_line(key=>'FILTER', ID=>$id)}));
+    $vcf->add_header_line({key=>'FILTER', ID=>$id,Description=>$desc});
+    return 0;
+}
+
+
+sub check_vcf_for_sample($$$) {
+    my ($vcf,$sample,$file) = @_;
+    my $is_found=0;
+    for ($vcf->get_samples()) {
+        $is_found=1 if($_ eq $sample);
+    }
+    errorX("Failed to find sample '$sample' in vcf file '$file'") unless($is_found);
+}
+
+
+
+my $depthFiltId="DP";
+
+
+# Runs all post-call vcf filters:
+#
+sub filterSnvFileList(\@$$$) {
+    my ($ifiles,$depthFilterVal,$acceptFileName,$isUseDepthFilter) = @_;
+
+    my $baseFiltId="BCNoise";
+    my $spanFiltId="SpanDel";
+    my $qFiltId="QSS_ref";
+
+    open(my $aFH,'>',$acceptFileName)
+      or errorX("Failed to open file: '$acceptFileName'");
+
+    my $is_first=1;
+    for my $ifile (@$ifiles) {
+        open(my $iFH,'<',"$ifile")
+          or errorX("Failed to open file: '$ifile'");
+        my $vcf = Vcf->new(fh=>$iFH);
+
+        # run some simple header validation on each vcf:
+        $vcf->parse_header();
+        check_vcf_for_sample($vcf,'NORMAL',$ifile);
+        check_vcf_for_sample($vcf,'TUMOR',$ifile);
+
+        if($is_first) {
+            # TODO: update vcf meta-data for chromosome-level filtered files
+            #
+            $vcf->remove_header_line(key=>"cmdline");
+            $vcf->add_header_line({key=>"cmdline",value=>$cmdline});
+            if($isUseDepthFilter) {
+                $vcf->add_header_line({key=>"maxDepth_$chrom",value=>$depthFilterVal});
+                add_vcf_filter($vcf,$depthFiltId,"Greater than ${depthFilterMultiple}x chromosomal mean depth in Normal sample");
+            }
+            add_vcf_filter($vcf,$baseFiltId,"Fraction of basecalls filtered at this site in either sample is at or above $snvMaxFilteredBasecallFrac");
+            add_vcf_filter($vcf,$spanFiltId,"Fraction of reads crossing site with spanning deletions in either sample exceeeds $snvMaxSpanningDeletionFrac");
+            add_vcf_filter($vcf,$qFiltId,"Normal sample is not homozygous ref or ssnv Q-score < $minQSSNT, ie calls with NT!=ref or QSS_NT < $minQSSNT");
+            print $aFH $vcf->format_header();
+            $is_first=0;
+        }
+
+        while(my $x=$vcf->next_data_hash()) {
+            my $norm=$x->{gtypes}->{NORMAL};
+            my $tumr=$x->{gtypes}->{TUMOR};
+
+            my %filters;
+
+            # normal depth filter:
+            my $normalDP=$norm->{DP};
+            if($isUseDepthFilter) {
+                $filters{$depthFiltId} = ($normalDP > $depthFilterVal);
+            }
+
+            # filtered basecall fraction:
+            my $normal_filt=($normalDP>0 ? $norm->{FDP}/$normalDP : 0);
+
+            my $tumorDP=$tumr->{DP};
+            my $tumor_filt=($tumorDP>0 ? $tumr->{FDP}/$tumorDP : 0);
+
+            $filters{$baseFiltId}=(($normal_filt >= $snvMaxFilteredBasecallFrac) or
+                                   ($tumor_filt >= $snvMaxFilteredBasecallFrac));
+
+            # spanning deletion fraction:
+            my $normalSDP=$norm->{SDP};
+            my $normalSpanTot=($normalDP+$normalSDP);
+            my $normalSpanDelFrac=($normalSpanTot>0 ? ($normalSDP/$normalSpanTot) : 0);
+
+            my $tumorSDP=$tumr->{SDP};
+            my $tumorSpanTot=($tumorDP+$tumorSDP);
+            my $tumorSpanDelFrac=($tumorSpanTot>0 ? ($tumorSDP/$tumorSpanTot) : 0);
+
+            $filters{$spanFiltId}=(($normalSpanDelFrac > $snvMaxSpanningDeletionFrac) or
+                                   ($tumorSpanDelFrac > $snvMaxSpanningDeletionFrac));
+
+            # Q-val filter:
+            $filters{$qFiltId}=(($x->{INFO}->{NT} ne "ref") or
+                                ($x->{INFO}->{QSS_NT} < $minQSSNT));
+
+            $x->{FILTER} = $vcf->add_filter($x->{FILTER},%filters);
+
+            print $aFH $vcf->format_line($x);
+        }
+
+        $vcf->close();
+        close($iFH);
+    }
+
+    close($aFH);
+}
+
+
+
+sub updateA2(\@$) {
+    my ($a2,$FH) = @_;
+    my $line=<$FH>;
+    unless(defined($line)) { errorX("Unexpected end of somatic indel window file"); }
+    chomp $line;
+    @$a2 = split("\t",$line);
+    unless(scalar(@$a2)) { errorX("Unexpected format in somatic indel window file"); }
+}
+
+
+
+sub filterIndelFileList(\@$$$) {
+    my ($ifiles,$depthFilterVal,$acceptFileName,$isUseDepthFilter) = @_;
+
+    my $repeatFiltId="Repeat";
+    my $iHpolFiltId="iHpol";
+    my $baseFiltId="BCNoise";
+    my $qFiltId="QSI_ref";
+
+    open(my $aFH,'>',$acceptFileName)
+      or errorX("Failed to open file: '$acceptFileName'");
+
+    my $is_first=1;
+    for my $ifile (@$ifiles) {
+        open(my $iFH,'<',"$ifile")
+          or errorX("Failed to open somatic indel file: '$ifile'");
+
+        my $iwfile = $ifile . ".window";
+        open(my $iwFH,'<',"$iwfile")
+          or errorX("Failed to open somatic indel window file: '$iwfile'");
+
+        my @a2; # hold window file data for one line in case we overstep...
+
+        my $vcf = Vcf->new(fh=>$iFH);
+
+        # run some simple header validation on each vcf:
+        $vcf->parse_header();
+        check_vcf_for_sample($vcf,'NORMAL',$ifile);
+        check_vcf_for_sample($vcf,'TUMOR',$ifile);
+
+        if($is_first) {
+            # TODO: update all vcf meta-data for chromosome-level filtered files
+            #
+            $vcf->remove_header_line(key=>"cmdline");
+            $vcf->add_header_line({key=>"cmdline",value=>$cmdline});
+            if($isUseDepthFilter) {
+                $vcf->add_header_line({key=>"maxDepth_$chrom",value=>$depthFilterVal});
+            }
+            $vcf->add_header_line({key=>'FORMAT', ID=>'DP50',Number=>1,Type=>'Float',Description=>'Average tier1 read depth within 50 bases'});
+            $vcf->add_header_line({key=>'FORMAT', ID=>'FDP50',Number=>1,Type=>'Float',Description=>'Average tier1 number of basecalls filtered from original read depth within 50 bases'});
+            $vcf->add_header_line({key=>'FORMAT', ID=>'SUBDP50',Number=>1,Type=>'Float',Description=>'Average number of reads below tier1 mapping quality threshold aligned across sites within 50 bases'});
+            if($isUseDepthFilter) {
+                add_vcf_filter($vcf,$depthFiltId,"Greater than ${depthFilterMultiple}x chromosomal mean depth in Normal sample");
+            }
+            add_vcf_filter($vcf,$repeatFiltId,"Sequence repeat of more than ${indelMaxRefRepeat}x in the reference sequence");
+            add_vcf_filter($vcf,$iHpolFiltId,"Indel overlaps an interupted homopolymer longer than ${indelMaxIntHpolLength}x in the reference sequence");
+            add_vcf_filter($vcf,$baseFiltId,"Average fraction of filtered basecalls within 50 bases of the indel exceeds $indelMaxWindowFilteredBasecallFrac");
+            add_vcf_filter($vcf,$qFiltId,"Normal sample is not homozygous ref or sindel Q-score < $minQSINT, ie calls with NT!=ref or QSI_NT < $minQSINT");
+            print $aFH $vcf->format_header();
+            $is_first=0;
+        }
+
+        while(my $x=$vcf->next_data_hash()) {
+            $vcf->add_format_field($x,'DP50');
+            $vcf->add_format_field($x,'FDP50');
+            $vcf->add_format_field($x,'SUBDP50');
+
+            my $norm=$x->{gtypes}->{NORMAL};
+            my $tumr=$x->{gtypes}->{TUMOR};
+
+            my $chrom=$x->{CHROM};
+            my $pos=int($x->{POS});
+
+            # get matching line from window file:
+            while((scalar(@a2)<2) or
+                  (($a2[0] le $chrom) and (int($a2[1]) < $pos))) {
+                updateA2(@a2,$iwFH);
+            }
+            unless(scalar(@a2) and ($a2[0] eq $chrom) and (int($a2[1]) == $pos))
+                { errorX("Can't find somatic indel window position.\nIndel line: " . $vcf->format_line($x) ); }
+
+            # add window data to vcf record:
+            #
+            $norm->{DP50} = $a2[2]+$a2[3];
+            $norm->{FDP50} = $a2[3];
+            $norm->{SUBDP50} = $a2[4];
+            $tumr->{DP50} = $a2[5]+$a2[6];
+            $tumr->{FDP50} = $a2[6];
+            $tumr->{SUBDP50} = $a2[7];
+
+            my %filters;
+
+            # normal depth filter:
+            my $normalDP=$norm->{DP};
+            if($isUseDepthFilter) {
+                $filters{$depthFiltId}=($normalDP > $depthFilterVal);
+            }
+
+            # ref repeat
+            my $refRep=$x->{INFO}->{RC};
+            $filters{$repeatFiltId}=(defined($refRep) and
+                                     ($refRep > $indelMaxRefRepeat));
+
+            # ihpol
+            my $iHpol=$x->{INFO}->{IHP};
+            $filters{$iHpolFiltId}=(defined($iHpol) and
+                                    ($iHpol > $indelMaxIntHpolLength));
+
+            # base filt:
+            my $normWinFrac=( $norm->{DP50} ? $norm->{FDP50}/$norm->{DP50} : 0 );
+            my $tumrWinFrac=( $tumr->{DP50} ? $tumr->{FDP50}/$tumr->{DP50} : 0 );
+            $filters{$baseFiltId}=( ($normWinFrac >= $indelMaxWindowFilteredBasecallFrac) or
+                                    ($tumrWinFrac >= $indelMaxWindowFilteredBasecallFrac) );
+
+            # Q-val filter:
+            $filters{$qFiltId}=(($x->{INFO}->{NT} ne "ref") or
+                                ($x->{INFO}->{QSI_NT} < $minQSINT));
+
+            $x->{FILTER} = $vcf->add_filter($x->{FILTER},%filters);
+
+            print $aFH $vcf->format_line($x);
+        }
+
+        $vcf->close();
+        close($iFH);
+        close($iwFH);
+    }
+
+    close($aFH);
+}
+
+
+
+my @ssnvFiles;
+my @sindelFiles;
+for my $binId (@$binList) {
+    my $ssnvFile = File::Spec->catfile($chromDir,'bins',$binId,'somatic.snvs.unfiltered.vcf');
+    my $sindelFile = File::Spec->catfile($chromDir,'bins',$binId,'somatic.indels.unfiltered.vcf');
+    checkFile($ssnvFile,"bin snv file");
+    checkFile($sindelFile,"bin indel file");
+    push @ssnvFiles,$ssnvFile;
+    push @sindelFiles,$sindelFile;
+}
+
+my $ssnvOutFile = File::Spec->catfile($chromDir,"somatic.snvs.vcf");
+filterSnvFileList(@ssnvFiles,$filterCoverage,$ssnvOutFile,$isUseDepthFilter);
+
+my $sindelOutFile = File::Spec->catfile($chromDir,"somatic.indels.vcf");
+filterIndelFileList(@sindelFiles,$filterCoverage,$sindelOutFile,$isUseDepthFilter);
+
+
+1;