changeset 2:7c35d3efd1e7

Deleted selected files

Binary file strelka2/.configureStrelkaWorkflow.pl.swp has changed

Binary file strelka2/.strelka.xml.swp has changed

Binary file strelka2/.strelka_wrapper.bash.swo has changed

Binary file strelka2/.strelka_wrapper.py.swp has changed

--- a/strelka2/configureStrelkaWorkflow.pl	Thu Sep 25 12:02:14 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,564 +0,0 @@
-#!/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
-
-configureStrelkaWorkflow.pl --tumor FILE --normal FILE --ref FILE --config FILE [options]
-
-This script configures the strelka workflow for somatic variant
-calling on matched tumor-normal BAM files. The configuration process
-will produce an analysis makefile and directory structure. The
-makefile can be used to run the analysis on a workstation or compute
-cluster via make/qmake or other makefile compatible process.
-
-=head1 ARGUMENTS
-
-=over 4
-
-=item --tumor FILE
-
-Path to tumor sample BAM file (required)
-
-=item --normal FILE
-
-Path to normal sample BAM file (required)
-
-=item --ref FILE
-
-Path to reference genome fasta (required)
-
-=item --config FILE
-
-Strelka configuration file. Default config files can be found in
-${STRELKA_INSTALL_ROOT}/etc/ for both ELAND and BWA alignments. (required)
-
-=back
-
-=head1 OPTIONS
-
-=over 4
-
-=item --output-dir DIRECTORY
-
-Root of the analysis directory. This script will place all
-configuration files in the analysis directory, and after configuration
-all results and intermediate files will be written within the analysis
-directory during a run. This directory must not already
-exist. (default: ./strelkaAnalysis)
-
-=back
-
-=cut
-
-use warnings FATAL => 'all';
-use strict;
-
-use Carp;
-$SIG{__DIE__} = \&Carp::confess;
-
-use Cwd qw(getcwd);
-use File::Spec;
-use Getopt::Long;
-use Pod::Usage;
-
-my $baseDir;
-my $libDir;
-BEGIN {
-    my $thisDir=(File::Spec->splitpath($0))[1];
-    $baseDir=$thisDir;#$baseDir=File::Spec->catdir($thisDir,File::Spec->updir());
-    $libDir=File::Spec->catdir($baseDir,'lib');
-}
-use lib $libDir;
-use Utils;
-
-if(getAbsPath($baseDir)) {
-    errorX("Can't resolve path for strelka_workflow install directory: '$baseDir'");
-}
-my $libexecDir=File::Spec->catdir($baseDir,'libexec');
-#my $optDir=File::Spec->catdir($baseDir,'opt');
-
-
-my $scriptName=(File::Spec->splitpath($0))[2];
-my $argCount=scalar(@ARGV);
-my $cmdline = join(' ',$0,@ARGV);
-
-
-sub usage() { pod2usage(-verbose => 1,
-                        -exitval => 2); }
-
-#
-# user configuration:
-#
-
-my ($tumorBam, $normalBam, $refFile, $configFile, $outDir);
-my $help;
-
-GetOptions( "tumor=s" => \$tumorBam,
-            "normal=s" => \$normalBam,
-            "ref=s" => \$refFile,
-            "config=s" => \$configFile,
-            "output-dir=s" => \$outDir,
-            "help|h" => \$help) || usage();
-
-usage() if($help);
-usage() unless($argCount);
-
-
-#
-# Validate input conditions:
-#
-
-sub checkFileArg($$) {
-   my ($file,$label) = @_;
-
-   errorX("Must specify $label file") unless(defined($file)); #raise an error if file not defined
-   checkFile($file,$label);
-}
-
-checkFileArg($tumorBam,"tumor BAM");
-checkFileArg($normalBam,"normal BAM");
-checkFileArg($refFile,"reference fasta");
-checkFileArg($configFile,"configuration ini");
-
-sub makeAbsoluteFilePaths(\$) {
-    my ($filePathRef) = @_;
-
-    my ($v,$fileDir,$fileName) = File::Spec->splitpath($$filePathRef);
-    if(getAbsPath($fileDir)) {
-        errorX("Can't resolve directory path for '$fileDir' from input file argument: '$$filePathRef'");
-    }
-    $$filePathRef = File::Spec->catfile($fileDir,$fileName);
-}
-
-makeAbsoluteFilePaths($tumorBam);
-makeAbsoluteFilePaths($normalBam);
-makeAbsoluteFilePaths($refFile);
-makeAbsoluteFilePaths($configFile);
-
-# also check for BAM index files:
-sub checkBamIndex($) {
-    my ($file) = @_;
-    my $ifile = $file . ".bai";
-    if(! -f $ifile) {
-        errorX("Can't find index for BAM file '$file'");
-    }
-}
-
-checkBamIndex($tumorBam);
-checkBamIndex($normalBam);
-
-
-sub checkFaIndex($) {
-    my ($file) = @_;
-    my $ifile = $file . ".fai";
-    if(! -f $ifile) {
-        errorX("Can't find index for fasta file '$file'");
-    }
-    # check that fai file isn't improperly formatted (a la the GATK bundle NCBI 37 fai files)
-    open(my $FH,"< $ifile") || errorX("Can't open fai file '$ifile'");
-    my $lineno=1;
-    while(<$FH>) {
-          chomp;
-          my @F=split();
-          if(scalar(@F) != 5) {
-              errorX("Unexpected format for line number '$lineno' of fasta index file: '$ifile'\n\tRe-running fasta indexing may fix the issue. To do so, run: \"samtools faidx $file\"");
-          }
-          $lineno++;
-    }
-    close($FH);
-}
-
-checkFaIndex($refFile);
-
-
-if(defined($outDir)) {
-    if(getAbsPath($outDir)) {
-        errorX("Can't resolve path for ouput directory: '$outDir'");
-    }
-} else {
-    $outDir=File::Spec->catdir(Cwd::getcwd(),'strelkaAnalysis');
-}
-
-if(-e $outDir) {
-    errorX("Output path already exists: '$outDir'");
-}
-
-if(getAbsPath($baseDir)) {
-    errorX("Can't resolve path for strelka install directory: '$baseDir'");
-}
-
-		#my $samtoolsDir = File::Spec->catdir($optDir,'samtools');
-checkDir($libexecDir,"strelka libexec");
-		#checkDir($samtoolsDir,"samtools");
-
-my $callScriptName = "callSomaticVariants.pl";
-my $filterScriptName = "filterSomaticVariants.pl";
-my $finishScriptName = "consolidateResults.pl";
-my $callScript = File::Spec->catfile($libexecDir,$callScriptName);
-my $filterScript = File::Spec->catfile($libexecDir,$filterScriptName);
-my $finishScript = File::Spec->catfile($libexecDir,$finishScriptName);
-my $countFasta = File::Spec->catfile($libexecDir,"countFastaBases");
-		#my $samtoolsBin = File::Spec->catfile($samtoolsDir,"samtools");
-checkFile($callScript,"somatic variant call script");
-checkFile($filterScript,"somatic variant filter script");
-checkFile($finishScript,"result consolidation script");
-checkFile($countFasta,"fasta scanner");
-#checkFile($samtoolsBin,"samtools");
-
-#
-# Configure bin runs:
-#
-checkMakeDir($outDir);
-
-#
-# Configure bin runs: open and validate config ini
-#
-my $config = parseConfigIni($configFile);
-
-sub checkConfigKeys($) {
-    my ($keyref) = @_;
-    for (@$keyref) {
-        errorX("Undefined configuration option: '$_'") unless(defined($config->{user}{$_}));
-    }
-}
-
-# these are the keys we need at configuration time:
-my @config_keys = qw(binSize);
-
-# these are additional keys we will need to run the workflow:
-# (note we don't check for (maxInputDepth,minTier2Mapq) for back compatibility with older config files)
-my @workflow_keys = qw(
-minTier1Mapq isWriteRealignedBam ssnvPrior sindelPrior ssnvNoise sindelNoise ssnvNoiseStrandBiasFrac
-ssnvQuality_LowerBound sindelQuality_LowerBound isSkipDepthFilters depthFilterMultiple
-snvMaxFilteredBasecallFrac snvMaxSpanningDeletionFrac indelMaxRefRepeat
-indelMaxWindowFilteredBasecallFrac indelMaxIntHpolLength);
-
-checkConfigKeys(\@config_keys);
-checkConfigKeys(\@workflow_keys);
-
-
-my $binSize = int($config->{user}{binSize});
-
-$config->{derived}{configurationCmdline} = $cmdline;
-$config->{derived}{normalBam} = $normalBam;
-$config->{derived}{tumorBam} = $tumorBam;
-$config->{derived}{refFile} = $refFile;
-$config->{derived}{outDir} = $outDir;
-
-#
-# Configure bin runs: check for consistent chrom info between BAMs and reference
-#
-sub getBamChromInfo($) {
-    my $file = shift;
-    my $cmd = "samtools view -H $file |";
-    open(my $FH,$cmd) || errorX("Can't open process $cmd");
-
-    my %info;
-    my $n=0;
-    while(<$FH>) {
-        next unless(/^\@SQ/);
-        chomp;
-        my @F = split(/\t/);
-        scalar(@F) >= 3 || errorX("Unexpected bam header for file '$file'");
-
-        my %h = ();
-        foreach (@F) {
-            my @vals = split(':');
-            $h{$vals[0]} = $vals[1];
-        }
-        $F[1] = $h{'SN'};
-        $F[2] = $h{'LN'};
-
-        my $size = int($F[2]);
-        ($size > 0) || errorX("Unexpected chromosome size '$size' in bam header for file '$file'");
-        $info{$F[1]}{size} = $size;
-        $info{$F[1]}{order} = $n;
-        $n++;
-    }
-    close($FH) || errorX("Can't close process $cmd");
-    return %info;
-}
-
-
-my %chromInfo = getBamChromInfo($normalBam);
-my @chroms = sort { $chromInfo{$a}{order} <=> $chromInfo{$b}{order} } (keys(%chromInfo));
-
-{
-    #consistency check:
-    my %tumorChromInfo = getBamChromInfo($tumorBam);
-    for my $chrom (@chroms) {
-        my $ln = $chromInfo{$chrom}{size};
-        my $tln = $tumorChromInfo{$chrom}{size};
-        my $order = $chromInfo{$chrom}{order};
-        my $torder = $tumorChromInfo{$chrom}{order};
-        unless(defined($tln) && ($tln==$ln) && ($torder==$order)) {
-            errorX("Tumor and normal BAM file headers disagree on chromosome: '$chrom'");
-        }
-        delete $tumorChromInfo{$chrom};
-    }
-    for my $chrom (keys(%tumorChromInfo)) {
-        errorX("Tumor and normal BAM file headers disagree on chromosome: '$chrom'");
-    }
-}
-
-
-my %refChromInfo;
-logX("Scanning reference genome");
-{
-    my $knownGenomeSize=0;
-    my $cmd="$countFasta $refFile |";
-    open(my $FFH,$cmd) || errorX("Failed to open process '$cmd'");
-
-    while(<$FFH>) {
-        chomp;
-        my @F = split(/\t/);
-        scalar(@F) == 4 || errorX("Unexpected value from '$cmd'");
-        $knownGenomeSize += int($F[2]);
-        $refChromInfo{$F[1]}{knownSize} = int($F[2]);
-        $refChromInfo{$F[1]}{size} = int($F[3]);
-    }
-    close($FFH) || errorX("Failed to close process '$cmd'");
-
-    #consistency check:
-    for my $chrom (@chroms) {
-        my $ln = $chromInfo{$chrom}{size};
-        my $rln = $refChromInfo{$chrom}{size};
-        unless(defined($rln) && ($rln==$ln)) {
-            errorX("BAM headers and reference fasta disagree on chromosome: '$chrom'");
-        }
-        $config->{derived}{"chrom_${chrom}_size"} = $rln;
-        $config->{derived}{"chrom_${chrom}_knownSize"} = $refChromInfo{$chrom}{knownSize};
-    }
-    $config->{derived}{chromOrder} = join("\t",@chroms);
-
-    $config->{derived}{knownGenomeSize} = $knownGenomeSize;
-}
-logX("Scanning reference genome complete");
-
-
-
-#
-# Configure bin runs: create directory structure
-#
-my $resultsDir = File::Spec->catdir($outDir,'results');
-checkMakeDir($resultsDir);
-if($config->{user}{isWriteRealignedBam}) {
-    my $bamDir = File::Spec->catdir($outDir,'realigned');
-    checkMakeDir($bamDir);
-}
-my $chromRootDir = File::Spec->catdir($outDir,'chromosomes');
-checkMakeDir($chromRootDir);
-for my $chrom (@chroms) {
-    my $chromDir = File::Spec->catdir($chromRootDir,$chrom);
-    checkMakeDir($chromDir);
-
-    my $chromRef = $chromInfo{$chrom};
-    $chromRef->{dir} = $chromDir;
-    $chromRef->{binList} = getBinList($chromRef->{size},$binSize);
-
-    my $binRootDir = File::Spec->catdir($chromDir,'bins');
-    checkMakeDir($binRootDir);
-
-    for my $binId ( @{$chromRef->{binList}} ) {
-        my $binDir = File::Spec->catdir($binRootDir,$binId);
-        checkMakeDir($binDir);
-    }
-}
-
-
-
-#
-# write run config file:
-#
-my $runConfigFile;
-{
-    my $cstr = <<END;
-;
-; Strelka workflow configuration file
-;
-; This is an automatically generated file, you probably don't want to edit it. If starting a new run,
-; input configuration templates (with comments) can be found in the Strelka etc/ directory.
-;
-END
-
-    $cstr .= writeConfigIni($config);
-
-    my $configDir = File::Spec->catdir($outDir,'config');
-    checkMakeDir($configDir);
-    $runConfigFile = File::Spec->catdir($configDir,'run.config.ini');
-    open(my $FH,"> $runConfigFile") || errorX("Can't open file '$runConfigFile'");
-    print $FH $cstr;
-    close($FH);
-}
-
-
-
-#
-# create makefile
-#
-my $makeFile = File::Spec->catfile($outDir,"Makefile");
-open(my $MAKEFH, "> $makeFile") || errorX("Can't open file: '$makeFile'");
-
-my $completeFile = "task.complete";
-
-print $MAKEFH <<ENDE;
-# This makefile was automatically generated by $scriptName
-#
-# Please do not edit.
-
-script_dir := $libexecDir
-call_script := \$(script_dir)/$callScriptName
-filter_script := \$(script_dir)/$filterScriptName
-finish_script := \$(script_dir)/$finishScriptName
-
-config_file := $runConfigFile
-
-analysis_dir := $outDir
-results_dir := \$(analysis_dir)/results
-
-ENDE
-
-print $MAKEFH <<'ENDE';
-
-complete_tag := task.complete
-
-finish_task := $(analysis_dir)/$(complete_tag)
-
-get_chrom_dir = $(analysis_dir)/chromosomes/$1
-get_chrom_task = $(call get_chrom_dir,$1)/$(complete_tag)
-get_bin_task = $(call get_chrom_dir,$1)/bins/$2/$(complete_tag)
-
-
-
-all: $(finish_task)
-	@$(print_success)
-
-
-define print_success
-echo;\
-echo Analysis complete. Final somatic calls can be found in $(results_dir);\
-echo
-endef
-
-
-# top level results target:
-#
-$(finish_task):
-	$(finish_script) --config=$(config_file) && touch $@
-
-
-# chromosome targets:
-#
-ENDE
-
-for my $chrom (@chroms) {
-
-    print $MAKEFH <<ENDE;
-chrom_${chrom}_task := \$(call get_chrom_task,$chrom)
-\$(finish_task): \$(chrom_${chrom}_task)
-\$(chrom_${chrom}_task):
-	\$(filter_script) --config=\$(config_file) --chrom=$chrom && touch \$@
-
-ENDE
-
-}
-
-print $MAKEFH <<ENDE;
-
-# chromosome bin targets:
-#
-ENDE
-
-for my $chrom (@chroms) {
-    for my $bin (@{$chromInfo{$chrom}{binList}}) {
-
-print $MAKEFH <<ENDE;
-chrom_${chrom}_bin_${bin}_task := \$(call get_bin_task,$chrom,$bin)
-\$(chrom_${chrom}_task): \$(chrom_${chrom}_bin_${bin}_task)
-\$(chrom_${chrom}_bin_${bin}_task):
-	\$(call_script) --config=\$(config_file) --chrom=$chrom --bin=$bin && touch \$@
-
-ENDE
-
-    }
-}
-
-
-# If the eval function is available, this is the way we could finish
-# the makefile without being so verbose but it doesn't look like qmake
-# understands this function.
-
-=cut
-
-print $MAKEFH <<ENDE;
-
-chroms := @chroms
-
-ENDE
-
-for my $chrom (@chroms) {
-    print $MAKEFH "${chrom}_bins := " . join(" ",@{$chromInfo{$chrom}{binList}}) . "\n";
-}
-
-print $MAKEFH <<'ENDE';
-
-define chrom_task_template
-chrom_$1_task := $(call get_chrom_task,$1)
-$(finish_task): $$(chrom_$1_task)
-$$(chrom_$1_task):
-	$$(filter_script) --config=$$(config_file) --chrom=$1 && touch $$@
-endef
-
-$(foreach c,$(chroms),$(eval $(call chrom_task_template,$c)))
-
-
-# chromosome bin targets:
-#
-define chrom_bin_task_template
-chrom_$1_bin_$2_task := $(call get_bin_task,$1,$2)
-$$(chrom_$1_task): $$(chrom_$1_bin_$2_task)
-$$(chrom_$1_bin_$2_task):
-	$$(call_script) --config=$$(config_file) --chrom=$1 --bin=$2 && touch $$@
-endef
-
-$(foreach c,$(chroms), \
-    $(foreach b,$($c_bins),$(eval $(call chrom_bin_task_template,$c,$b))) \
- )
-
-ENDE
-
-=cut
-
-
-
-print <<END;
-
-
-Successfully configured analysis and created makefile '$makeFile'.
-
-To run the analysis locally using make, run:
-
-make -C $outDir
-
-...or:
-
-cd $outDir
-make
-
-END
-
-1;
-
-__END__
-

Binary file strelka2/lib/.Utils.pm.swp has changed

--- a/strelka2/lib/Utils.pm	Thu Sep 25 12:02:14 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,172 +0,0 @@
-
-=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/>.
-
-=cut
-
-
-package Utils;
-
-use base 'Exporter';
-
-our @EXPORT = qw(
-        errorX logX executeCmd checkFile checkDir checkMove
-        getAbsPath checkMakeDir getBinList
-        parseConfigIni writeConfigIni
-    );
-
-use warnings FATAL => 'all';
-use strict;
-
-use Carp;
-use Cwd qw(realpath);
-use File::Copy qw(move);
-use File::Path qw(mkpath);
-
-
-sub errorX($) {
-    confess "\nERROR: " . $_[0] . "\n\n";
-}
-
-sub logX($) {
-    print STDERR "INFO: " . $_[0] . "\n";
-}
-
-
-sub executeCmd($;$) {
-    my $cmd = shift;
-    my $isVerbose = shift;
-
-    logX("Running: '$cmd'") if(defined($isVerbose) and $isVerbose);
-    system($cmd) == 0
-      or errorX("Failed system call: '$cmd'");
-}
-#return an error if file does not exist 
-sub checkFile($;$) {
-    my $file = shift;
-    return if(-f $file);
-    my $label = shift;
-    errorX("Can't find" . (defined($label) ? " $label" : "") . " file: '$file'");
-}
-#return an error if file does not Exist
-sub checkDir($;$) {
-    my $dir = shift;
-    return if(-d $dir);
-    my $label = shift;
-    errorX("Can't find" . (defined($label) ? " $label" : "") . " directory: '$dir'");
-}
-
-sub checkMove($$) {
-    my ($old,$new) = @_;
-    move($old,$new) || errorX("File move failed: $!\n\tAttempting to move '$old' to '$new'");
-}
-
-
-
-
-=item getAbsPath($path)
-
-This procedure attempts to convert a path provided by the user on the
-command line into an absolute path. It should be able to handle "~"
-paths and conventional relative paths using ".." or ".". Resolution of
-links should follow the convention of "Cwd::realpath".
-
-B<Parameters:>
-
-    $dirRef         - path (converted to absolute path in place)
-
-B<Returns:>
-
-    returns zero if successful, non-zero otherwise.
-
-=cut
-sub getAbsPath(\$) {
-    my ($dirRef) = @_;
-    my @tmp=glob($$dirRef);
-    return 1 if(scalar(@tmp) != 1);
-    my $ret = Cwd::realpath($tmp[0]);
-    return 1 if !$ret && !($ret = File::Spec->rel2abs($tmp[0]));
-    $$dirRef = $ret;
-    return 0;
-}
-
-
-#verify path is not a file, then create a directory with this name if does not exist
-sub checkMakeDir($) {
-    my $dir = shift;
-    unless (-e $dir) {
-        File::Path::mkpath($dir) || errorX("Can't create directory '$dir'");
-    } else {
-        errorX("Path is not a directory '$dir'\n") unless(-d $dir);
-    }
-}
-
-
-
-sub getBinList($$) {
-    my ($chromSize,$binSize) = @_;
-
-    my $nm1 = (($chromSize-1) / $binSize);
-    return [ map {sprintf("%04i",$_)} (0..$nm1) ];
-}
-
-
-
-sub parseConfigError($$) {
-    my ($file,$line) = @_;
-    errorX("Config file '$file' contains unexpected line '$line'\n");
-}
-
-#lis le fichier de config, si la ligne est de type : some space + [ some character ] + some space then register ther character in $section. (   [user]   , then $section=user).   
-sub parseConfigIni($) {
-    my $file = shift;
-    my %config;
-    open(my $FH,"< $file") || errorX("Can't open config file '$file'");
-    my $section = "noSection";
-    while(<$FH>) {
-        next if(/^[;#]/);
-        next if(/^\s*$/);
-        chomp;
-        my $line=$_;
-        my @ncl = split(/[;#]/);
-        next unless(scalar(@ncl));
-        my $nc = $ncl[0];
-        if($nc =~ /^\s*\[([^\]]*)\]\s*$/) {
-            $section = $1;
-            next;
-        }
-        my ($key,$val) = map { s/^\s+//; s/\s+$//; $_ } split(/=/,$nc,2);
-        unless(defined($key) && defined($val) && ($key ne "")) { parseConfigError($file,$line); }
-
-        $config{$section}{$key} = $val;
-    }
-    close($FH);
-    return \%config;
-}
-
-
-# minimal ini stringifier:
-#
-sub writeConfigIni($) {
-    my $config = shift;
-    my $val = "";
-    for my $section (sort(keys(%$config))) {
-        $val .= "\n[$section]\n";
-        for my $key (sort(keys(%{$config->{$section}}))) {
-            $val .= "$key = " . $config->{$section}{$key} . "\n";
-        }
-    }
-    return $val;
-}
-
-
-1;

--- a/strelka2/libexec/callSomaticVariants.pl	Thu Sep 25 12:02:14 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,241 +0,0 @@
-#!/usr/bin/env perl
-print "\n";
-print @INC;
-print "\n";
-=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
-
-callSomaticVariants.pl [options] | --help
-
-=head2 SUMMARY
-
-Run the somatic variant caller for snvs and indels on a single
-chromosome bin.
-
-=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;
-BEGIN {
-print "\n";
-print @INC;
-print "\n";
-
-    my $thisDir=(File::Spec->splitpath($0))[1];
-    $baseDir=File::Spec->catdir($thisDir,File::Spec->updir());
-    $libDir=File::Spec->catdir($baseDir,'lib');
-}
-use lib $libDir;
-use Utils;
-
-if(getAbsPath($baseDir)) {
-    errorX("Can't resolve path for strelka_workflow install directory: '$baseDir'");
-}
-my $libexecDir=File::Spec->catdir($baseDir,'libexec');
-#my $optDir=File::Spec->catdir($baseDir,'opt');
-
-
-my $scriptName=(File::Spec->splitpath($0))[2];
-my $argCount=scalar(@ARGV);
-my $cmdline = join(' ',$0,@ARGV);
-
-
-my ($chrom, $binId, $configFile);
-my $help;
-
-GetOptions(
-            "chrom=s" => \$chrom,
-            "bin=s" => \$binId,
-            "config=s" => \$configFile,
-            "help|h" => \$help) or pod2usage(2);
-
-pod2usage(2) if($help);
-pod2usage(2) unless(defined($chrom));
-pod2usage(2) unless(defined($binId));
-pod2usage(2) unless(defined($configFile));
-
-
-
-#
-# check all fixed paths (not based on commandline arguments):
-#
-checkDir($baseDir);
-checkDir($libexecDir);
-#checkDir($optDir);
-
-my $strelkaBin=File::Spec->catdir($libexecDir,'strelka2');
-checkFile($strelkaBin,"strelka binary");
-#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(knownGenomeSize tumorBam normalBam refFile outDir)) {
-    errorX("Undefined configuration option: '$_'") unless(defined($config->{derived}{$_}));
-}
-
-# we skip maxInputDepth,minTier2Mapq here to allow older config files
-for (qw(minTier1Mapq isWriteRealignedBam binSize ssnvPrior sindelPrior
-        ssnvNoise sindelNoise ssnvNoiseStrandBiasFrac)) {
-    errorX("Undefined configuration option: '$_'") unless(defined($config->{user}{$_}));
-}
-
-my $outDir = $config->{derived}{outDir};
-my $binDir = File::Spec->catdir($outDir,'chromosomes',$chrom,'bins',$binId);
-checkDir($outDir,"output");
-checkDir($binDir,"output bin");
-
-
-my $tumorBam = $config->{derived}{tumorBam};
-my $normalBam = $config->{derived}{normalBam};
-my $refFile = $config->{derived}{refFile};
-checkFile($tumorBam,"tumor BAM");
-checkFile($normalBam,"normal BAM");
-checkFile($refFile,"reference");
-
-
-# pull out some config options for convenience:
-my $binSize=$config->{user}{binSize};
-my $isWriteRealignedBam=$config->{user}{isWriteRealignedBam};
-my $knownGenomeSize = $config->{derived}{knownGenomeSize};
-
-
-my $begin = (int($binId)*$binSize)+1;
-my $end = ((int($binId)+1)*$binSize);
-#my $end = $begin+100000;  #debug mode
-
-my $useroptions = $config->{user};
-
-# set previous default value if an older config file is being used:
-if(! defined($useroptions->{minTier2Mapq})) {
-    $useroptions->{minTier2Mapq} = 5;
-}
-
-
-#
-# setup the strelka command-line:
-#
-my $strelka_base_opts= "-clobber" .
-" -filter-unanchored" .
-" -min-paired-align-score " . $useroptions->{minTier1Mapq} .
-" -min-single-align-score 10" .
-" -min-qscore 0" .
-" -report-range-begin $begin -report-range-end $end" .
-" -samtools-reference '$refFile'" .
-" -max-window-mismatch 3 20 -print-used-allele-counts" .
-" -bam-seq-name '" . $chrom . "'" .
-" -genome-size $knownGenomeSize" .
-" -max-indel-size 50" .
-" -indel-nonsite-match-prob 0.5" .
-" --min-contig-open-end-support 35" .
-" --somatic-snv-rate " . $useroptions->{ssnvPrior} .
-" --shared-site-error-rate " . $useroptions->{ssnvNoise} .
-" --shared-site-error-strand-bias-fraction " . $useroptions->{ssnvNoiseStrandBiasFrac} .
-" --somatic-indel-rate " . $useroptions->{sindelPrior} .
-" --shared-indel-error-rate " . $useroptions->{sindelNoise} .
-" --tier2-min-single-align-score " . $useroptions->{minTier2Mapq} .
-" --tier2-min-paired-align-score " . $useroptions->{minTier2Mapq} .
-" --tier2-single-align-score-rescue-mode" .
-" --tier2-mismatch-density-filter-count 10" .
-" --tier2-no-filter-unanchored" .
-" --tier2-indel-nonsite-match-prob 0.25" .
-" --tier2-include-singleton" .
-" --tier2-include-anomalous";
-
-
-my $somSnvFile='somatic.snvs.unfiltered.vcf';
-my $somIndelFile='somatic.indels.unfiltered.vcf';
-
-my $cmd =  "$strelkaBin $strelka_base_opts" .
-" -bam-file " . $normalBam .
-" --tumor-bam-file " . $tumorBam .
-" --somatic-snv-file " . File::Spec->catfile($binDir,$somSnvFile) .
-" --somatic-indel-file " . File::Spec->catfile($binDir,$somIndelFile) .
-" --variant-window-flank-file 50 " . File::Spec->catfile($binDir,$somIndelFile . '.window');
-
-
-sub ualignFile($) {
-    return File::Spec->catfile($binDir,$_[0] . ".unsorted.realigned.bam");
-}
-sub alignFile($) {
-    return File::Spec->catfile($binDir,$_[0] . ".realigned");
-}
-
-
-if(exists($useroptions->{maxInputDepth}) && ($useroptions->{maxInputDepth} > 0)) {
-    $cmd .= " --max-input-depth " . $useroptions->{maxInputDepth};
-}
-
-
-if($isWriteRealignedBam) {
-    $cmd .= " -realigned-read-file " . ualignFile("normal") .
-            " --tumor-realigned-read-file " . ualignFile("tumor");
-}
-
-if(defined($useroptions->{extraStrelkaArguments})){
-    my $arg=$useroptions->{extraStrelkaArguments};
-    if($arg !~ /^\s*$/) {
-        $cmd .= " " . $arg;
-    }
-}
-
-# this file contains site stats that used to be printed on stdout:
-#
-$cmd .=
-" --report-file " . File::Spec->catfile($binDir,'strelka.stats');
-
-$cmd .=
-" >| " . File::Spec->catfile($binDir,'strelka.stdout') .
-" 2>| " . File::Spec->catfile($binDir,'strelka.stderr');
-
-
-executeCmd($cmd,0);
-
-
-if($isWriteRealignedBam) {
-    for my $label (qw(normal tumor)) {
-        my $ufile = ualignFile($label);
-        if( -f $ufile ) {
-            my $afile = alignFile($label);
-            my $cmd = "samtools sort " . $ufile .  " " . $afile;
-            executeCmd($cmd,0);
-            unlink($ufile);
-        } else {
-            logX("Can't find unsorted realigned BAM file: '$ufile'");
-        }
-    }
-}
-
-
-1;
-
-__END__
-
-

--- a/strelka2/libexec/consolidateResults.pl	Thu Sep 25 12:02:14 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,276 +0,0 @@
-#!/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__
-

Binary file strelka2/libexec/countFastaBases has changed

--- a/strelka2/libexec/filterSomaticVariants.pl	Thu Sep 25 12:02:14 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,435 +0,0 @@
-#!/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;

Binary file strelka2/libexec/strelka2 has changed

--- a/strelka2/strelka2.xml	Thu Sep 25 12:02:14 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-<tool id="strelka88" name="Strelka good interface but no dependencies">
-
-  <description>Strelka good interface but no dependencies</description>
-  <command interpreter="python">strelka_wrapper.py --tumorBam $tumorBam --normalBam $normalBam --refFile $refFile
-   #if $configuration.configuration_switch == 'Default':
-	--configFile 				Default
-   #else if $configuration.configuration_switch == 'Path':
-        --configFile				$configuration.configFile
-   #else:
-        --configFile				Custom
-        --depthFilterMultiple 			$configuration.depthFilterMultiple
-        --snvMaxFilteredBasecallFrac		$configuration.snvMaxFilteredBasecallFrac
-        --snvMaxSpanningDeletionFrac 		$configuration.snvMaxSpanningDeletionFrac
-        --indelMaxRefRepeat			$configuration.indelMaxRefRepeat
-        --indelMaxWindowFilteredBasecallFrac	$configuration.indelMaxWindowFilteredBasecallFrac
-        --indelMaxIntHpolLength			$configuration.indelMaxIntHpolLength
-        --ssnvPrior				$configuration.ssnvPrior
-        --sindelPrior				$configuration.sindelPrior
-        --ssnvNoise				$configuration.ssnvNoise
-        --sindelNoise				$configuration.sindelNoise
-        --ssnvNoiseStrandBiasFrac		$configuration.ssnvNoiseStrandBiasFrac
-        --minTier1Mapq				$configuration.minTier1Mapq
-        --minTier2Mapq				$configuration.minTier2Mapq
-        --ssnvQuality_LowerBound		$configuration.ssnvQuality_LowerBound
-        --sindelQuality_LowerBound		$configuration.sindelQuality_LowerBound
-        --isWriteRealignedBam			$configuration.isWriteRealignedBam
-        --binSize 				$configuration.binSize
-        --isSkipDepthFilters			$configuration.isSkipDepthFilters
-        --maxInputDepth 			$configuration.maxInputDepth
-        #if $configuration.extra_arguments.extra_arguments_switch == 'Yes':
-	      --extraStrelkaArguments 		    $configuration.extra_arguments.extraStrelkaArguments
-        #end if
-   #end if
-   </command>
-
-   <inputs>
-    <param format="bam" name="tumorBam" type="data" label="Tumor bam file"/>
-    <param format="bam" name="normalBam" type="data" label="Normal bam file"/>
-    <param format="fasta" name="refFile" type="data" label="ref fasta file"/>
-
-    <conditional name="configuration">
-      <param name="configuration_switch" type="select" label="how do you want to configure strelka">
-        <option value="Default" selected="true">Default</option>
-	<option value="Path">Use a config file</option>
-        <option value="Custom">Custom</option>
-      </param>
-      <when value="Default">
-        <!-- do nothing -->
-      </when>
-      <when value="Path">
-        <param format="ini" name="configFile" type="data" label="config file"/>
-      </when>
-      <when value="Custom">
-        <param name="binSize" type="integer" value="25000000" label="binSize" />
-        <param name="minTier1Mapq" type="integer" value="20" min="0" max="40" help="between 0 and 40" label="minTier1Mapq" />
-        <param name="minTier2Mapq" type="integer" value="5" min="0" max="5" help="between 0 and 5" label="minTier2Mapq" />
-        <param name="isWriteRealignedBam" type="integer" value="0" label="isWriteRealignedBam" />
-        <param name="ssnvPrior" type="float" value="0.000001" label="ssnvPrior" />
-        <param name="sindelPrior" type="float" value="0.000001" label="sindelPrior" />
-        <param name="ssnvNoise" type="float" value="0.0000005" label="ssnvNoise" />
-        <param name="sindelNoise" type="float" value="0.000001" label="sindelNoise" />
-        <param name="ssnvNoiseStrandBiasFrac" type="float" value="0.5" label="ssnvNoiseStrandBiasFrac" />
-        <param name="ssnvQuality_LowerBound" type="integer" value="15" label="ssnvQuality_LowerBound" />
-        <param name="sindelQuality_LowerBound" type="integer" value="30" label="sindelQuality_LowerBound" />
-        <param name="isSkipDepthFilters" type="integer" value="1" label="isSkipDepthFilters" />
-        <param name="depthFilterMultiple" type="float" value="3.0" label="depthFilterMultiple" />
-        <param name="snvMaxFilteredBasecallFrac" type="float" value="0.4" label="snvMaxFilteredBasecallFrac" />
-        <param name="snvMaxSpanningDeletionFrac" type="float" value="0.75" label="snvMaxSpanningDeletionFrac" />
-        <param name="indelMaxRefRepeat" type="integer" value="8" label="indelMaxRefRepeat" />
-        <param name="indelMaxWindowFilteredBasecallFrac" type="float" value="0.3" label="indelMaxWindowFilteredBasecallFrac" />
-        <param name="indelMaxIntHpolLength" type="integer" value="14" label="indelMaxIntHpolLength" />
-        <param name="maxInputDepth" type="integer" value="10000" label="maxInputDepth" />
-        <conditional name="extra_arguments">
-	  <param name="extra_arguments_switch" type="select" label="Do you Want to add extraStrelkaArguments?">
-            <option value="No" selected="true">No</option>
-            <option value="Yes">Yes</option>
-          </param>
-          <when value="No">
-            <!-- do nothing -->
-          </when>
-          <when value="Yes"> 
-	    <param name="extraStrelkaArguments" type="text" value="" label="extraStrelkaArguments" />
-          </when>
-        </conditional>
-      </when>
-    </conditional>  
-    <conditional name="conf_file">
-      <param name="conf_file_switch" type="select" label="output conf_file ?">
-        <option value="No" selected="true">No</option>
-        <option value="Yes">Yes</option>
-      </param>
-    </conditional>
-
-
-
-
-  </inputs>
-
-  <outputs>
-    <data format="vcf" name="output1_vcf" label="${tool.name} on ${on_string}(passed.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.snvs.vcf"/>
-    <data format="vcf" name="output2_vcf" label="${tool.name} on ${on_string}(passed.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.indels.vcf"/>
-    <data format="vcf" name="output3_vcf" label="${tool.name} on ${on_string}(all.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.snvs.vcf"/>
-    <data format="vcf" name="output4_vcf" label="${tool.name} on ${on_string}(all.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.indels.vcf"/>
-    <data name="conf_file.ini" label="conf_file.ini" from_work_dir="StrelkaAnalysis/tmp/config.ini">
-      <filter>conf_file.conf_file_switch == "Yes"</filter>
-    </data>
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="normalBam" ftype="bam" value="NA12891_dupmark_chr20_region.bam"/>
-      <param name="tumorBam" ftype="bam" value="NA12892_dupmark_chr20_region.bam"/>
-      <param name="refFile" ftype="fasta" value="chr20_860k_only.fa"/>
-      <param name="configuration_switch" value="Default"/>
-      <output name="output1_vcf" file="passed.somatic.snvs.vcf"/>
-      <output name="output2_vcf" file="passed.somatic.indels.vcf"/>
-      <output name="output3_vcf" file="all.somatic.snvs.vcf"/>
-      <output name="output4_vcf" file="all.somatic.indels.vcf"/>
-    </test>
-  </tests>
-
-  <help>
-Strelka, a method for somatic SNV and small indel detectipon from sequencing data of matched tumor-normal samples.
-  </help>
-
-</tool>

--- a/strelka2/strelka_config.sample	Thu Sep 25 12:02:14 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,139 +0,0 @@
-
-;
-; User configuration options for Strelka somatic small-variant caller
-; workflow:
-;
-
-[user]
-
-;
-; isSkipDepthFilters should be set to 1 to skip depth filtration for
-; whole exome or other targeted sequencing data
-;
-isSkipDepthFilters = 1
-
-;
-; strelka will not accept input reads above this depth (they will be skipped
-; until the depth drops below this value). Set this value <= 0 to disable
-; this feature. Using this filter will bound memory usage given extremely high
-; depth input, but may be problematic in high-depth targeted sequencing
-; applications.
-;
-maxInputDepth = 10000
-
-;
-; If the depth filter is not skipped, all variants which occur at a
-; depth greater than depthFilterMultiple*chromosome mean depth will be
-; filtered out.
-;
-depthFilterMultiple = 3.0
-
-;
-; Somatic SNV calls are filtered at sites where greater than this
-; fraction of basecalls have been removed by the mismatch density
-; filter in either sample.
-;
-snvMaxFilteredBasecallFrac = 0.4
-
-;
-; Somatic SNV calls are filtered at sites where greater than this
-; fraction of overlapping reads contain deletions which span the SNV
-; call site.
-;
-snvMaxSpanningDeletionFrac = 0.75
-
-;
-; Somatic indel calls are filtered if they represent an expansion or
-; contraction of a repeated pattern with a repeat count greater than
-; indelMaxRefRepeat in the reference (ie. if indelMaxRefRepeat is 8,
-; then the indel is filtered when it is an expansion/contraction of a
-; homopolymer longer than 8 bases, a dinucleotide repeat longer than
-; 16 bases, etc.)
-;
-indelMaxRefRepeat = 8
-
-;
-; Somatic indel calls are filtered if greater than this fraction of
-; basecalls in a window extending 50 bases to each side of an indel's
-; call position have been removed by the mismatch density filter.
-;
-indelMaxWindowFilteredBasecallFrac = 0.3
-
-;
-; Somatic indels are filtered if they overlap ’interrupted
-; homopolymers’ greater than this length. The term 'interrupted
-; homopolymer' is used to indicate the longest homopolymer which can
-; be found intersecting or adjacent to the called indel when a single
-; non-homopolymer base is allowed.
-;
-indelMaxIntHpolLength = 14
-
-;
-; prior probability of a somatic snv or indel
-;
-ssnvPrior = 0.000001
-sindelPrior = 0.000001
-
-;
-; probability of an snv or indel noise allele 
-;
-; NB: in the calling model a noise allele is shared in tumor and
-; normal samples, but occurs at any frequency.
-;
-ssnvNoise = 0.0000005
-sindelNoise = 0.000001
-
-;
-; Fraction of snv noise attributed to strand-bias.
-;
-; It is not recommended to change this setting. However, if it is
-; essential to turn the strand bias penalization off, the following is
-; recommended:
-; Assuming the current value of ssnvNoiseStrandBiasFrac is 0.5,
-; (1) set ssnvNoiseStrandBiasFrac = 0
-; (2) divide the current ssnvNoise value by 2
-;
-ssnvNoiseStrandBiasFrac = 0.5
-
-;
-; minimum MAPQ score for PE reads at tier1:
-;
-minTier1Mapq = 20
-
-;
-; minimum MAPQ score for PE and SE reads at tier2:
-;
-minTier2Mapq = 5
-
-;
-; Somatic quality score (QSS_NT, NT=ref) below which somatic SNVs are
-; marked as filtered:
-;
-ssnvQuality_LowerBound = 15
-
-;
-; Somatic quality score (QSI_NT, NT=ref) below which somatic indels
-; are marked as filtered:
-;
-sindelQuality_LowerBound = 30
-
-;
-; Optionally write out read alignments which were altered during the
-; realignment step. At the completion of the workflow run, the
-; realigned reads can be found in:
-;
-; ${ANALYSIS_DIR}/realigned/{normal,tumor}.realigned.bam
-;
-isWriteRealignedBam = 0
-
-;
-; Jobs are parallelized over segments of the reference genome no larger
-; than this size:
-;
-binSize = 25000000
-
-;
-; Additional arguments passed to strelka.
-;
-extraStrelkaArguments =
-

--- a/strelka2/strelka_wrapper.py	Thu Sep 25 12:02:14 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,201 +0,0 @@
-#!/usr/bin/env python
-#Dan Blankenberg
-
-"""
-A wrapper script for running the GenomeAnalysisTK.jar commands.
-"""
-
-from __future__ import print_function
-import sys, argparse, os, tempfile, subprocess, shutil
-from binascii import unhexlify
-from string import Template
-from galaxy import eggs
-#import pkg_resources; pkg_resources.require( "bx-python" )
-
-#GALAXY_EXT_TO_GATK_EXT = { 'gatk_interval':'intervals', 'bam_index':'bam.bai', 'gatk_dbsnp':'dbSNP', 'picard_interval_list':'interval_list' } #items not listed here will use the galaxy extension as-is
-#GALAXY_EXT_TO_GATK_FILE_TYPE = GALAXY_EXT_TO_GATK_EXT #for now, these are the same, but could be different if needed
-#DEFAULT_GATK_PREFIX = "gatk_file"
-#CHUNK_SIZE = 2**20 #1mb
-#
-#
-def cleanup_before_exit( tmp_dir ):
-    if tmp_dir and os.path.exists( tmp_dir ):
-        shutil.rmtree( tmp_dir )
-
-def _create_config(args, config_path):
-    conf_file = open(config_path, "w")
-    conf_file.write("[user]\n")
-    for option in args:
-        if not option in ["tumorBam", "normalBam", "refFile", "configFile"] and args[option]!=None:
-    	    conf_file.write("%s=%s\n" % (option, args[option]))
-    conf_file.close()
-
-def my_Popen(cmd, prefix_for_stderr_name, tmp_dir, msg_error):
-    stderr_name = tempfile.NamedTemporaryFile( prefix = prefix_for_stderr_name ).name
-    proc = subprocess.Popen( args=cmd, shell=True, stderr=open( stderr_name, 'wb' ) )
-    return_code = proc.wait()                          
-    if return_code:
-	for line in open( stderr_name ):
-           print(line, file=sys.stderr)
-	os.unlink( stderr_name ) #clean up
- 	cleanup_before_exit( tmp_dir )
- 	raise Exception( msg_error )
-    else:
-        os.unlink( stderr_name )
-
-def index_bam_files( bam_filenames, tmp_dir ):
-    for bam_filename in bam_filenames:
-        bam_index_filename = "%s.bai" % bam_filename
-        print("bam_filename is: " + bam_filename + " bam_index_filename is: " + bam_index_filename + " test is: %s" % os.path.exists(bam_index_filename))
-        if not os.path.exists( bam_index_filename ):
-            #need to index this bam file
-            command = 'samtools index %s %s' % ( bam_filename, bam_index_filename )
-            my_Popen( command, "bam_index_stderr", tmp_dir, "Error during indexation of fasta file :" + bam_filename)
-
-def index_fasta_files( fasta_filenames, tmp_dir ):
-    for fasta_filename in fasta_filenames:
-        fasta_index_filename = "%s.fai" % fasta_filename
-        print("fasta_filename is: " + fasta_filename + " fasta_index_filename is: " + fasta_index_filename + " test is: %s" % os.path.exists(fasta_index_filename))
-        if not os.path.exists( fasta_index_filename ):
-            #need to index this bam file
-            command = 'samtools faidx %s %s' % ( fasta_filename, fasta_index_filename )
-            my_Popen( command, "fasta_index_stderr", tmp_dir, "Error during indexation of fasta file :" + fasta_filename)
-
-def __main__():
-    #Parse Command Line  OPTPARSE DEPRECIATED USE ARGPARSE INSTEAD
-    #MKTEMP DEPRECIATED USE MKDTlizations#EMP INSTEAD
-        
-    root_dir= "/home/galaxyusr/data/galaxy_dist/tools/strelka2"
-    expected_dir="for_tests"
-    job_dir=os.getcwd()
-    analysis_dir=job_dir + "/StrelkaAnalysis"
-    config_script=root_dir + "/configureStrelkaWorkflow.pl"
-    tmp_dir = "tmp"  #tempfile.mkdtemp( prefix='tmp-strelkaAnalysis-' )
-    config_ini = "%s/config.ini" % (tmp_dir)
-
-    print("root_dir: " + root_dir + "\njob_dir :" + job_dir + "\nanalysis_dir :" + analysis_dir + "\nconfig_script :" + config_script + "\ntmp_dir :" + tmp_dir + "\nconfig_ini :" +  config_ini)
-   
-    #manage parsing
-    parser = argparse.ArgumentParser()                                             
-    parser.add_argument( '-t', '--tumorBam', help='path to tumor bam file', required = False )
-    parser.add_argument( '-n', '--normalBam', help='path to tumor bam file', required = False )   
-    parser.add_argument( '-r', '--refFile', help='path to tumor bam file', required = False )
-    parser.add_argument( '-c', '--configFile', help='path to tumor bam file', required = False )
-    parser.add_argument( '--depthFilterMultiple', help='path to tumor bam file', required = False )
-    parser.add_argument( '--snvMaxFilteredBasecallFrac', help='path to tumor bam file', required = False )
-    parser.add_argument( '--snvMaxSpanningDeletionFrac', help='path to tumor bam file', required = False )
-    parser.add_argument( '--indelMaxRefRepeat', help='path to tumor bam file', required = False )
-    parser.add_argument( '--indelMaxWindowFilteredBasecallFrac', help='path to tumor bam file', required = False )
-    parser.add_argument( '--indelMaxIntHpolLength', help='path to tumor bam file', required = False )
-    parser.add_argument( '--ssnvPrior', help='path to tumor bam file', required = False )
-    parser.add_argument( '--sindelPrior', help='path to tumor bam file', required = False )
-    parser.add_argument( '--ssnvNoise', help='path to tumor bam file', required = False )
-    parser.add_argument( '--sindelNoise', help='path to tumor bam file', required = False )
-    parser.add_argument( '--ssnvNoiseStrandBiasFrac', help='path to tumor bam file', required = False )
-    parser.add_argument( '--minTier1Mapq', help='path to tumor bam file', required = False )
-    parser.add_argument( '--minTier2Mapq', help='path to tumor bam file', required = False )
-    parser.add_argument( '--ssnvQuality_LowerBound', help='path to tumor bam file', required = False )
-    parser.add_argument( '--sindelQuality_LowerBound', help='path to tumor bam file', required = False )
-    parser.add_argument( '--isWriteRealignedBam', help='path to tumor bam file', required = False )
-    parser.add_argument( '--binSize', help='path to tumor bam file', required = False )
-    parser.add_argument( '--extraStrelkaArguments', help='path to tumor bam file', required = False )
-    parser.add_argument( '--isSkipDepthFilters', help='path to tumor bam file', required = False )
-    parser.add_argument( '--maxInputDepth', help='path to tumor bam file', required = False )
-    args = parser.parse_args()
-
-    #verifying eveything's ok
-    if not os.path.isfile(config_script):
-    	sys.exit("ERROR: The strelka workflow must be built prior to running. See installation instructions in '$root_dir/README'")
-    print("configuring...", file=sys.stdout)
-    if os.path.exists(analysis_dir):
-	sys.exit("'" + analysis_dir + "' already exist, if you are executing this tool from galaxy it should not happen")
-    
-
-    # creating index if needed
-    os.environ['PATH']= root_dir + "/opt/samtools:" + os.environ['PATH']
-    bam_filenames = [ args.tumorBam, args.normalBam ]
-    index_bam_files( bam_filenames, tmp_dir )
-    fasta_files = [ args.refFile ]
-    index_fasta_files( fasta_files, tmp_dir )
-    
-    #creating config file if needed
-    if args.configFile == "Custom":
-    	_create_config(vars(args), config_ini)
-    elif args.configFile == "Default":
-        cmdbash="cp %s %s" % (root_dir + "/strelka_config.sample", config_ini)
-        my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed")
-    else:
-    	if not os.path.exists(args.configFile):
-	     print( "The path to your configuration File seems to be wrong, use another one or custom option", file=sys.stderr)
-    	cmdbash="cp %s %s" % (args.configFile, config_ini)
-        my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed")
-
-
-
-
-    #configuration of workflow
-    cmd="%s --tumor=%s --normal=%s --ref=%s --config=%s --output-dir=%s" % (config_script, args.tumorBam, args.normalBam, args.refFile, config_ini, analysis_dir)
-    print( "**** Starting configuration.")
-    print( "**** Configuration cmd: '" + cmd + "'")
-    my_Popen( cmd, "cinfugation_stderr", tmp_dir, "Error during configuration !")
-    print("completed configuration")
-    
-    #run the workflow !
-    cmd="make -C " + analysis_dir
-    print("**** starting workflow.")
-    print("**** workflow cmd: '" + cmd + "'")
-    my_Popen( cmd, "workflow_stderr", tmp_dir, "Error during workflow execution !")   
-    print("**** completed workflow execution")
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-#bam_filenames = []
-#    if options.datasets:
-#        for ( dataset_arg, filename, galaxy_ext, prefix ) in options.datasets:
-#            gatk_filename = filename_from_galaxy( filename, galaxy_ext, target_dir = tmp_dir, prefix = prefix )#return the link to the dataset that has been created in the function
-#            if dataset_arg:
-#                cmd = '%s %s "%s"' % ( cmd, gatk_filetype_argument_substitution( dataset_arg, galaxy_ext ), gatk_filename )
-#            if galaxy_ext == "bam":
-#                bam_filenames.append( gatk_filename )
-#    #set up stdout and stderr output options
-#    stdout = open_file_from_option( options.stdout, mode = 'wb' )
-#    stderr = open_file_from_option( options.stderr, mode = 'wb' )
-#    #if no stderr file is specified, we'll use our own
-#    if stderr is None:
-#        stderr = tempfile.NamedTemporaryFile( prefix="strelka-stderr-", dir=tmp_dir )
-#    
-#    proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
-#    return_code = proc.wait()
-#    
-#    if return_code:
-#        stderr_target = sys.stderr
-#    else:
-#        stderr_target = sys.stdout
-#    stderr.flush()
-#    stderr.seek(0)
-#    while True:
-#        chunk = stderr.read( CHUNK_SIZE )
-#        if chunk:
-#            stderr_target.write( chunk )
-#        else:
-#            break
-#    stderr.close()
-#    #generate html reports
-#    if options.html_report_from_directory:
-#        for ( html_filename, html_dir ) in options.html_report_from_directory:
-#            html_report_from_directory( open( html_filename, 'wb' ), html_dir )
-#    
-#    cleanup_before_exit( tmp_dir )
-
-if __name__=="__main__": __main__()

--- a/strelka2/tool_dependencies.xml	Thu Sep 25 12:02:14 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="samtools" version="0.1.18">
-    <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="vcftools" version="0.1.11">
-    <repository changeset_revision="710efaae2ff8" name="package_vcftools_0_1_11" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-  </package>
-</tool_dependency>