Mercurial > repos > niels > annovar_yaml_wrapper

changeset 7:1119dc7a2f67 draft

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Deleted selected files
author niels
date Tue, 14 May 2019 05:07:46 -0400
parents a55510bb8478
children 9d6e7d2ddbb7
files annovar_yaml/YAML_annovar.yml annovar_yaml/YAML_arguments_annovar.yml annovar_yaml/annovar_yaml.pl annovar_yaml/annovar_yaml.xml
diffstat 4 files changed, 0 insertions(+), 1250 deletions(-) [+]
line wrap: on
line diff
--- a/annovar_yaml/YAML_annovar.yml	Tue May 14 05:07:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,66 +0,0 @@
-GENERAL:
-  - APPLICATION: 'annovar'
-    PATHSCRIPTS: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
-    CODING_ANNOVAR: 'coding_annovar.pl'
-    TABLE_ANNOVAR: 'table_annovar.pl'
-    LOCATION_DATABASE: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
-    DOT2UNDERLINE: 'yes'
-    NASTRING: '.'
-    OTHERINFO: 'yes'
-    POLISH: 'yes'
-    REMOVE: 'yes'
-    THREAD: '8'
-    INPUTFORMAT: 'vcfinput'
-    SPECIES: 'human'
-    BUILD: 'hg19'
-ANALYSIS:
-  DATABASES:
-  - NAME: 'cosmic84'
-    PROTOCOL: 'cosmic'
-    VERSION: '84'
-    COMMENT: '20190221'
-    AVAILABLE: 'yes'
-    REQUIRED: 'yes'
-    OPERATION: 'f' 
-    COLSWANTED: '4'
-  - NAME: 'refgene19'
-    PROTOCOL: 'refgene'
-    VERSION: '19' 
-    AVAILABLE: 'yes'
-    REQUIRED: 'yes'
-    COMMENT: '20190210'
-    OPERATION: 'g'
-    HGVS: 'yes'
-    SPLICING: '6'
-    EXONSPLIC: 'yes'
-  - NAME: 'ncbiRefSeq_UMCU'
-    PROTOCOL: 'ncbiRefSeq'
-    VERSION: '_UMCU'
-    AVAILABLE: 'yes'
-    REQUIRED: 'yes'
-    COMMENT: "100519"
-    OPERATION: 'g'
-    HGVS: 'yes'
-    SPLICING: '6'
-    EXONSPLIC: 'yes'
-  - NAME: 'avsnp150'
-    PROTOCOL: 'avsnp'
-    VERSION: '150'
-    AVAILABLE: 'yes'
-    REQUIRED: 'yes'
-    OPERATION: 'f'
-    COLSWANTED: '1'
-  - NAME: 'clinvar_20180603'
-    PROTOCOL: 'clinvar'
-    VERSION: '_20180603'
-    AVAILABLE: 'yes'
-    REQUIRED: 'yes'
-    OPERATION: 'f'
-    COLSWANTED: '5'
-  - NAME: 'class100519'
-    PROTOCOL: 'class'
-    VERSION: '100519'
-    AVAILABLE: 'yes'
-    REQUIRED: 'yes'
-    OPERATION: 'f'
-    COLSWANTED: '1'
--- a/annovar_yaml/YAML_arguments_annovar.yml	Tue May 14 05:07:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,111 +0,0 @@
-GENERAL:
-  - APPLICATION: 'annovar'
-    PATHSCRIPTS: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
-    CODING_ANNOVAR: 'coding_annovar.pl '
-    TABLE_ANNOVAR: 'table_annovar.pl '
-    LOCATION_DATABASE: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
-    DOT2UNDERLINE:
-      yes: '--dot2underline '
-      no: ''
-    NASTRING: '--nastring . '
-    OTHERINFO:
-      yes: '--otherinfo '
-      no: ''
-    POLISH:
-      yes: '--polish '
-      no: ''
-    REMOVE:
-      yes: '--remove '
-      no: ''
-    THREAD: '--thread 8 '
-    INPUTFORMAT:
-      vcfinput: '--vcfinput '
-    SPECIES:
-      human: 'humandb '
-      mouse: 'mousedb '
-    BUILD: '--buildver hg19 '
-ANALYSIS:
-  DATABASES:
-    - NAME: 'cosmic84'
-      PROTOCOL: 'cosmic'
-      VERSION: '84'
-      COMMENT: '20190221' 
-      AVAILABLE:
-        yes: '1'
-        no: '0'
-      REQUIRED:
-        yes: '1'
-        no: '0'
-      OPERATION: 'f'
-      COLSWANTED: '--colswanted 4 '
-    - NAME: 'refgene19'
-      PROTOCOL: 'refgene'
-      VERSION: '19' 
-      COMMENT: '20190210'  
-      AVAILABLE:
-        yes: '1'
-        no: '0'
-      REQUIRED:
-        yes: '1'
-        no: '0'
-      OPERATION: 'g'
-      HGVS:
-        yes: '--hgvs '
-        no: ''
-      SPLICING: '--splicing 6 '
-      EXONSPLIC:  
-        yes: '--exonicsplicing '
-        no: ''
-    - NAME: 'ncbiRefSeq_UMCU'
-      PROTOCOL: 'ncbiRefSeq'
-      VERSION: '_UMCU'
-      AVAILABLE:
-        yes: '1'
-        no: '0'
-      REQUIRED:
-        yes: '1'
-        no: '0'
-      COMMENT: "100519"
-      OPERATION: 'g'
-      HGVS:
-        yes: '--hgvs '
-        no: ''
-      SPLICING: '--splicing 6 '
-      EXONSPLIC:
-        yes: '--exonicsplicing '
-        no: ''
-    - NAME: 'avsnp150'
-      PROTOCOL: 'avsnp'
-      VERSION: '150'
-      AVAILABLE:
-        yes: '1'
-        no: '0'
-      REQUIRED:
-        yes: '1'
-        no: '0'
-      OPERATION: 'f'
-      COLSWANTED: '--colswanted 1 '
-    - NAME: 'clinvar_20180603'
-      PROTOCOL: 'clinvar'
-      VERSION: '_20180603'
-      COMMENT: 'blah'
-      AVAILABLE:
-        yes: '1'
-        no: '0'
-      REQUIRED:
-        yes: '1'
-        no: '0'
-      OPERATION: 'f'
-      COLSWANTED: '--colswanted 5 '
-    - NAME: 'class100519'
-      PROTOCOL: 'class'
-      VERSION: '100519'
-      AVAILABLE:
-        yes: '1'
-        no: '0'
-      REQUIRED:
-        yes: '1'
-        no: '0'
-      OPERATION: 'f'
-      COLSWANTED: '--colswanted 1 '
-      
--- a/annovar_yaml/annovar_yaml.pl	Tue May 14 05:07:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1047 +0,0 @@
-#/usr/bin/perl
-
-#perl modules use
-use YAML;
-use YAML::Tiny;
-use YAML::XS 'LoadFile';
-use Data::Dumper;
-#use Data::YAML::Writer;
-use Getopt::Long;
-use strict;
-
-#input required
-#two modes run and edit
-#Basis Yaml file [default required]
-#Yaml out file [required in edit mode]
-#species [default required]
-#build [default required]
-#protocol [default required]
-#protocolversion [default required]
-
-#basic paramters
-my $edit = "0";
-my $run = "0";
-my $application = "0";
-my $parameter_yml = "YAML_arguments_annovar.yml";
-my $inyml;
-my $outyml;
-my $invcf;
-my $outvcf;
-my $yml_hash_arguments;
-my %yml_hash_arguments;
-my $yml_hash;
-my %yml_hash;
-my $yml_hash_edit;
-my %yml_hash_edit;
-my $in;
-my $in2;
-my %in;
-my %in2;
-my $writer;
-
-#parameter applications
-my %annovarparameters_array;
-my %annovarparameters_single;
-my $annovarparameters_array;
-my $annovarparameters_single;
-
-#Strings used as input parameters
-#my $input_general_location_database;
-#my $input_general_dir_scripts;
-#my $input_general_location_scripts_coding_annovar;
-#my $input_general_location_scripts_table_annovar;
-my $input_annovar_build;
-my $input_annovar_species;
-my $inprotocol;
-my $inprotocolversion;
-my @inprotocol;
-my @inprotocolversion;
-
-my $input_general_settings_dot2underline;
-my $input_general_settings_nastring;
-my $input_general_settings_otherinfo;
-my $input_general_settings_polish;
-my $input_general_settings_remove;
-my $input_general_settings_thread;
-my $input_general_settings_inputformat;
-
-my $input_databases_available;
-my $input_databases_required;
-
-my $input_databases_colswanted;
-my $input_databases_exonicsplic;
-my $input_databases_hgvs;
-my $input_databases_operation;
-my $input_databases_splicing;
-my @input_databases_colswanted;
-my @input_databases_exonicsplic;
-my @input_databases_hgvs;
-my @input_databases_operation;
-my @input_databases_splicing;
-
-#other variables
-my $script;
-my $type;
-my $count;
-my $column_build;
-my $column_species;
-my @column_build;
-my @column_species;
-my $pattern;
-my $pattern2;
-my $match;
-my $match_value;
-my @match_value;
-my @readonly;
-my %editinyml;
-
-#Fixed values for searching hashes
-my $level5 = "DATABASES";
-
-#parameters to build command
-my $protocol;
-my @protocol;
-my $operation;
-my $argument;
-
-GetOptions (
-	#Required input
-	'protocol=s' => \$inprotocol,
-	'protocolversion=s' => \$inprotocolversion,
-	'script=s' => \$script,
-	'invcf=s' => \$invcf,
-	'outvcf=s' => \$outvcf,
-	'application=s' => \$application,
-        'inyml=s' => \$inyml,
-        'outyml=s' => \$outyml,
-        'build=s'       => \$input_annovar_build,
-        'species=s'   => \$input_annovar_species,
-	#Optional input
-	'edit' => \$edit,
-	'run' => \$run,
-	#variables in GENERAL
-	'dot2underline=s'   => \$input_general_settings_dot2underline,
-	'nastring=s'   => \$input_general_settings_nastring,
-	'otherinfo=s'   => \$input_general_settings_otherinfo,
-	'polish=s'   => \$input_general_settings_polish,
-	'remove=s'   => \$input_general_settings_remove,
-	'thread=s'   => \$input_general_settings_thread,
-	'inputformat=s'  => \$input_general_settings_inputformat,
-	#variables in DATABASES
-	'colswanted=s'   => \$input_databases_colswanted,
-	'exonicsplic=s'   => \$input_databases_exonicsplic,
-	'hgvs=s'   => \$input_databases_hgvs,
-	'operation=s'   => \$input_databases_operation,
-	'splicing=s'   => \$input_databases_splicing,
-);
-
-
-#inactive options
-#       'drequired=s'   => \$input_databases_required,
-#       'davail=s'   => \$input_databases_available,
-
-#       'gpathdatabase=s'   => \$input_general_location_database,
-#	'gpathscripts=s'   => \$input_general_dir_scripts,
-#       'gpathcodannovar=s'   => \$input_general_location_scripts_coding_annovar,
-#       'gpathtabannovar=s'   => \$input_general_location_scripts_table_annovar,
-
-#Check input parameters
-#Do some checks whether all required arguments are given
-
-#some code
-
-#arrays with all application specific parameters
-#make sure keys are unique to allow for parsing of yml! 
-
-%annovarparameters_array = (
-	"COLSWANTED" => "$input_databases_colswanted",
-	"EXONICSPLIC" => "$input_databases_exonicsplic",
-	"HGVS" => "$input_databases_hgvs",
-	"OPERATION" => "$input_databases_operation",
-	"SPLICING" => "$input_databases_splicing",
-);
-
-%annovarparameters_single = (
-	"DOT2UNDERLINE" => "$input_general_settings_dot2underline",
-	"NASTRING" => "$input_general_settings_nastring",
-	"OTHERINFO" => "$input_general_settings_otherinfo",
-	"POLISH" => "$input_general_settings_polish",
-	"REMOVE" => "$input_general_settings_remove",
-	"THREAD" => "$input_general_settings_thread",
-	"INPUTFORMAT" => "$input_general_settings_inputformat",
-);
-
-#parameter not allowed to be edited in yml
-@readonly = ("hg19","human","mouse","mm10","annovar","VERSION","TABLE_ANNOVAR","refgene","cosmic");
-
-
-#converting string into arrays
-@inprotocol = split (",", $inprotocol);
-print "version $inprotocolversion\n";
-@inprotocolversion = split (",", $inprotocolversion);
-@input_databases_colswanted = split (",", $input_databases_colswanted);
-@input_databases_exonicsplic = split (",", $input_databases_exonicsplic);
-@input_databases_hgvs = split (",", $input_databases_hgvs );
-@input_databases_operation = split (",", $input_databases_operation);
-@input_databases_splicing = split (",", $input_databases_splicing);
-
-#$in = $inyml;
-#openyml_read($in);
-#$in = $inyml;
-#load($in);
-
-#check if combination of application,species, build and protocol exists
-#$count = "0";
-#%in = $yml_hash;
-#foreach (@inprotocol) {
-#print "protocol $inprotocol[$count]\n";  
-#$pattern = "$application:ANALYSIS:$input_annovar_species:$input_annovar_build:DATABASES:$inprotocol[$count]$inprotocolversion[$count]:NAME $inprotocol[$count]$inprotocolversion[$count]";
-#@pattern = ("GENERAL:species", "GENERAL:build", "GENERAL:protocol");
-#foreach @pattern {
-#  parse($in, $_);
-#  if ($match =~ /^1$/) { print "Present!\n"; };
-#  $count++;
-#  }
-#}
-
-#$in = $inyml;
-#openyml_read($in);
-#$in = $inyml;
-#load_edit($in);
-
-#Editing section first single values, next arrays
-#print "Starting editing of strings...\n";
-#foreach my $key (keys %annovarparameters_single) {
-#    my $innermatch = "0";
-    #print "Key: $key\n";
-#    foreach my $innerkey (@readonly) {
-#        if ($key =~ /^$innerkey$/) {
-	    #print "Value not allowed to be changed!\n";  
-#            $innermatch++; };
-#        }
-#    if ($innermatch >= 1) {
-#	print "Skipping: $key\n";
-	#Do nothing
-#    } else { 
-#    my $value = $annovarparameters_single{$key};
-#    if ($value !~ /^$/) {
-#        print "key:$key value:$value\n";
-#        $pattern = "^($application:.{1,}:$key)";
-#	print "pattern: $pattern\n";
-#        %in = $yml_hash_edit; 
-#        parse($in, $pattern);
-#        print "editing value...: $match_value\n";
-#        @match_value = split (':', $match_value);
-# 	 my $max = scalar @match_value;
-# 	 $count = "0";
-#        foreach (@match_value) {
-#	   if ($count == $max-1) {
-#               print "$_\n";
-#	       $_ =~ s/^.{1,}$/$value/g;
-#	       print "after: $_ \n";
-#	   }
-#	   $count++;
-#	}
-#	print "max $max\n";
-#        if ( $max == 4 ) {
-#            $yml_hash_edit->{$match_value[0]}{$match_value[1]}{$match_value[2]} = $match_value[3]
-#        }
-#    }
-#    } 
-#}
-
-#print "\n";
-#my $checkkey;
-
-#allow processing of arrays as well
-#print "Starting editing of array values...\n";
-#foreach my $key ( keys %annovarparameters_array) {
-#    $count = "0";
-    #print "COUNT: $count\n";
-    #print "KEY: $key\n";
-#    my @key = split (',', $key);
-#    foreach my $innerkey (@key) {
-#        my $innermatch = "0";
-#        foreach $checkkey (@readonly) {
-#            if ($innerkey =~ /^$checkkey$/) {
-                #Do nothing
-#                $innermatch++; };
-#            }
-#        if ($innermatch >= 1) {
-#            print "innerkey: $innerkey skipped\n";
-
-#       } else {
-#        my $value = $annovarparameters_array{$key};
-#	if ($value !~ /^$/ ) {
-#	    print "Value: $value\n";
-#	    my @value = split (',', $value);
-#	    my $innercount = "0";
-#            foreach my $innervalue (@value) {
-#		if ( $innervalue !~ /^$/ ) {
-#	            print "\nkey: $key innerkey: $innerkey check: $checkkey value: $innervalue\n";
-#	            print "innercount: $innercount\n";
-#	            $pattern = "^($application:.{1,}:$input_annovar_species:$input_annovar_build:.{1,}:@inprotocol[$innercount]$inprotocolversion[$innercount]:$key)";
-#                    print "pattern: $pattern\n";
-#	            %in = $yml_hash_edit;
-#	            parse($in, $pattern);
-#		    undef %in;
-#	            print "editing value...: $match_value\n";
-#	                if ($match =~ /^1$/) {
-#                            @match_value = split (':', $match_value);
-#                            my $max = scalar @match_value;
-#                            #$count = "0";
-#                            foreach (@match_value) { 
-#				print "count: $count\n";
-#		                if ($count == $max-1) {
-#		                    print "empty_check: $_ \n";
-#			            $_ =~ s/^.{1,}$/$value[$innercount]/g;
-#			            print "empty_check_after: $_ \n";
-#		                }                                   
-#		                print "Max: $max\n";
-#                                $count++;
-#		            }
-#			    print "change: $value[$innercount]\n";
-#			    print "Max: $max\n";
-#                            if ( $max == 9 ) {
-#                                $yml_hash_edit->{$match_value[0]}{$match_value[1]}{$match_value[2]}{$match_value[3]}{$match_value[4]}{$match_value[5]}{$match_value[6]}{$match_value[7]} = $match_value[8]; 
-#                           }
-#	                } else {
-#
-#	                     if ($match =~ /^0$/) {   
-#	                         $pattern = "^($application:.{1,}:$input_annovar_species:$input_annovar_build:.{1,}:@inprotocol[$innercount]:$inprotocolversion[$innercount])";
-#                                 %in = $yml_hash_edit;
-#				 parse($in, $pattern);          
-#				 undef %in;
-#	                         print "editing value...: $match_value\n";
-#	                         if ($match > 1) {
-#                                     @match_value = split (':', $match_value); 
-#	                             my $max = scalar @match_value;
-#				     $count = "0";
-#                                     print "Max: $max\n";
-#                                     if ( $max == 9 ) {
-#                                         $yml_hash_edit->{$match_value[0]}{$match_value[1]}{$match_value[2]}{$match_value[3]}{$match_value[4]}{$match_value[5]}{$match_value[6]}{$innerkey} = "$innervalue";
-#                                     }
-# 	                         }    
-#	                     }
-#	                }          
-#		} else {
-#                #Do nothing no arugment supplied  
-#		}
-#	    $innercount++;
-#	    }
-#        } else {
-#	#Do nothing no argument supplied
-#        }
-#	}
-#    }
-#$count++;
-#print "\n";
-#}
-
-#print "\nFinished editing...\n";
-
-#Create second yml file with change values originating from cli
-#$in = $outyml;
-#openyml_write($in);
-#%in = $yml_hash_edit; 
-#writeyml_edit($in);
-#$in = $outyml;
-#load($outyml);
-#print "Finished loading second yml...\n";
-
-#Load ymlhash with arguments
-#$in = $parameter_yml;
-#openyml_read($in);
-#$in = $parameter_yml;
-#load_arguments($in);
-#print "Finished loading arguments...\n";
-
-#Build command for application
-
-################### stuff to replace with loop
-
-#Starting with Annovar
-#$count = "0";
-#foreach (@inprotocol) {
-#$protocol .= "$_$inprotocolversion[$count]";
-#print "protocol $inprotocol\n";
-#print "protocol_version $inprotocolversion\n";
-#if ($count+1 >= scalar @inprotocol) { } else { $protocol .= "','"; };
-#$count++; 
-#}
-
-#Make new array with protocol plus version
-#@protocol = split (",", $protocol); 
-#foreach (@protocol) {
-#print "print value: $_\n";
-#}
-
-#Required as input value, not pickup from yaml file!
-#$operation = $input_databases_operation;
-#$operation =~ s/,/','/g;
-
-#$count= "0";
-#foreach (@inprotocol) {
-#if ( $_ =~ /refgene/ ) {
-#print "Entering refgene...\n";
-#$argument .= "$yml_hash_arguments->{$application}{ANALYSIS}{$input_annovar_species}{$input_annovar_build}{DATABASES}{$protocol[$count]}{ARG}{HGVS}{$yml_hash_edit->{$application}{ANALYSIS}{$input_annovar_species}{$input_annovar_build}{DATABASES}{$protocol[$count]}{ARG}{HGVS}} ";
-#$argument .= "--splicing $yml_hash_edit->{$application}{ANALYSIS}{$input_annovar_species}{$input_annovar_build}{DATABASES}{$protocol[$count]}{ARG}{SPLICING} "; 
-#$argument .= "$yml_hash_arguments->{$application}{ANALYSIS}{$input_annovar_species}{$input_annovar_build}{DATABASES}{$protocol[$count]}{ARG}{EXONSPLIC}{$yml_hash_edit->{$application}{ANALYSIS}{$input_annovar_species}{$input_annovar_build}{DATABASES}{$protocol[$count]}{ARG}{EXONSPLIC}}";
-#if ($count+1 >= scalar @inprotocol) { } else { $argument .= "','"; };
-#} elsif ( $_ =~ /cosmic/ ) {
-#print "Entering cosmic...\n";
-#$argument .= "--colswanted $yml_hash_edit->{$application}{ANALYSIS}{$input_annovar_species}{$input_annovar_build}{DATABASES}{$protocol[$count]}{ARG}{COLSWANTED}";
-#if ($count+1 >= scalar @inprotocol) { } else { $argument .= "','"; };
-#} 
-#$count++;
-#}
-
-#print "$argument\n";
-
-#Put content to print in arrays
-#my @protocol_values = ("$inprotocol","$operation","$argument");
-#my @values = ("$yml_hash_edit->{$application}{GENERAL}{PATHSCRIPTS}","$yml_hash_edit->{$application}{GENERAL}{$script}","$yml_hash_edit->{$application}{GENERAL}{LOCATION_DATABASE}","$input_annovar_build","$yml_hash_arguments->{$application}{GENERAL}{REMOVE}{$yml_hash_edit->{$application}{GENERAL}{REMOVE}}","$yml_hash_arguments->{$application}{GENERAL}{DOT2UNDERLINE}{$yml_hash_edit->{$application}{GENERAL}{DOT2UNDERLINE}}","$yml_hash_arguments->{$application}{GENERAL}{OTHERINFO}{$yml_hash_edit->{$application}{GENERAL}{OTHERINFO}}","$yml_hash_edit->{$application}{GENERAL}{NASTRING}","$yml_hash_arguments->{$application}{GENERAL}{INPUTFORMAT}{$yml_hash_edit->{$application}{GENERAL}{INPUTFORMAT}}","$yml_hash_edit->{$application}{GENERAL}{THREAD}","$yml_hash_arguments->{$application}{GENERAL}{POLISH}{$yml_hash_edit->{$application}{GENERAL}{POLISH}}");
-
-#foreach (@protocol_values) { print "line array1: $_\n" };
-#foreach (@values) { print "line array2: $_\n" };
-
-#Build actual command
-#my $annovar_command = "perl $values[0]$values[1] $invcf $values[2] --buildver $values[3] $values[4] --protocol \'$protocol_values[0]\' --operation \'$protocol_values[1]\' $values[5] $values[6] --nasstring \'$values[7]\' $values[8] --arg \'$protocol_values[2]\' --thread $values[9] $values[10] --outfile $outvcf";
-
-################### end of static code
-
-#Printing/execting command!
-#print "$annovar_command\n";
-
-#Execute command
-#Do some stuff to actual run the command...
-
-#Build command
-
-#my @parameters_test = $yml_hash->{ANALYSIS}{DATABASES};
-#foreach (@parameters_test) {
-#print "value: $_\n";
-#}  
-#my $test_hash = $yml_hash->{ }{map};
-
-#print "value: $yml_hash->{ANALYSIS}{DATABASES}\n";
-
-#Fill hashes with input yaml files
-openyml_read ($parameter_yml);
-openyml_read ($inyml);
-load ($inyml, %yml_hash, $yml_hash);
-load_arguments ($parameter_yml, %yml_hash_arguments, $yml_hash_arguments);
-
-#Building annovar command:
-my $application = 'annovar';
-
-my $ncbiRefSeq = 'ncbiRefSeq';
-my $cosmic = 'cosmic';
-my $dbsnp = 'avsnp';
-my $clinvar = 'clinvar';
-my $class = 'class';
-
-my $ncbiRefSeq_version = '_UMCU';
-my $cosmic_version = '84';
-my $dbsnp_version = '150';
-my $clinvar_version = '_20180603';
-my $class_version = '100519';
-
-#species input fixed
-my $input_annovar_species = "human";
-
-#Defined in input
-#my $invcf = "/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/input_vcfs/prepared_vcfs/PA-AI-201812-154T_norm_2.vcf ";
-#my $outvcf = "/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/input_vcfs/prepared_vcfs/PA-AI-201812-154T_norm_2_out.vcf ";
-
-my $language = 'perl ';
-
-my $parse1 = 'parse1';
-my $parse2 = 'parse2';
-
-my $application_path = "$application,APPLICATION,GENERAL";
-
-my $ncbiRefSeq_path = "$ncbiRefSeq$ncbiRefSeq_version,NAME,ANALYSIS,DATABASES";
-my $cosmic_path = "$cosmic$cosmic_version,NAME,ANALYSIS,DATABASES";
-my $dbsnp_path = "$dbsnp$dbsnp_version,NAME,ANALYSIS,DATABASES";
-my $clinvar_path = "$clinvar$clinvar_version,NAME,ANALYSIS,DATABASES";
-my $class_path = "$class$class_version,NAME,ANALYSIS,DATABASES";
-
-#blocks to build command
-my @command_building_blocks = ( 
-"$language",
-"$parse1,PATHSCRIPTS,$application_path",
-"$parse1,TABLE_ANNOVAR,$application_path",
-"$invcf",
-"$parse1,LOCATION_DATABASE,$application_path",
-"$parse1,SPECIES,$application_path",
-"$parse1,BUILD,$application_path",
-"$parse1,REMOVE,$application_path",
-"--protocol \'",
-"$parse2,NAME,$ncbiRefSeq_path",
-"\,",
-"$parse2,NAME,$cosmic_path",
-"\,",
-"$parse2,NAME,$dbsnp_path",
-"\,",
-"$parse2,NAME,$clinvar_path",
-"\,",
-"$parse2,NAME,$class_path",
-"\' ",
-"--operation \'",
-"$parse2,OPERATION,$ncbiRefSeq_path",
-"\'",
-"\,",
-"\'",
-"$parse2,OPERATION,$cosmic_path",
-#"\'\,\'",
-"\'",
-"\,",
-"\'",
-"$parse2,OPERATION,$dbsnp_path",
-#"\'\,\'",
-"\'",
-"\,",
-"\'",
-"$parse2,OPERATION,$clinvar_path",
-#"\'\,\'",
-"\'",
-"\,",
-"\'",
-"$parse2,OPERATION,$class_path",
-"\' ",
-"$parse1,DOT2UNDERLINE,$application_path",
-"$parse1,OTHERINFO,$application_path",
-"$parse1,NASTRING,$application_path",
-"$parse1,INPUTFORMAT,$application_path",
-"--arg \'",
-"$parse2,HGVS,$ncbiRefSeq_path",
-"$parse2,SPLICING,$ncbiRefSeq_path",
-"$parse2,EXONSPLIC,$ncbiRefSeq_path",
-#"\'\,\'",
-"\'",
-"\,",
-"\'",
-"$parse2,COLSWANTED,$cosmic_path",
-#"\'\,\'",
-"\'",
-"\,",
-"\'",
-"$parse2,COLSWANTED,$dbsnp_path",
-#"\'\,\'",
-"\'",
-"\,",
-"\'",
-"$parse2,COLSWANTED,$clinvar_path",
-#"\'\,\'",
-"\'",
-"\,",
-"\'",
-"$parse2,COLSWANTED,$class_path",
-"\' ",
-"$parse1,THREAD,$application_path",
-"$parse1,POLISH,$application_path",
-"-outfile $outvcf "); 
-
-print "\n";
-
-#Setup variables for processing
-my $lookup;
-my %input;
-my $input;
-my $match1;
-my $in_key;
-my $in_value;
-my $in_lookup;
-my ($pattern1, $pattern2, $pattern3, $pattern4, $pattern5);
-
-#Empty command
-my $test_command = "";
-
-foreach (@command_building_blocks) {
-  $in = $inyml;
-  $in2 = $parameter_yml;
-  #print "loop1:$_\n";
-  if ( $_ =~ /^,$/ ) {
-    print "$_ is separator and does not require matching!\n\n";
-    $test_command .= "$_";
-    next;
-  }
-  my @values = split /\,/, $_;
-  foreach (@values) {
-    if ( $_ =~ /^parse1/ ) {
-    #print "parse1: $in, $in2, $values[1], $values[2], $values[3], $values[4], %yml_hash, %yml_hash_arguments, $yml_hash, $yml_hash_arguments\n";
-    parse1 ($in, $in2, $values[1], $values[2], $values[3], $values[4], %yml_hash, %yml_hash_arguments, $yml_hash, $yml_hash_arguments);
-    print "parse1_out:$lookup...\n";
-    $test_command .= "$lookup";
-    $lookup = '';
-    $input = '';
-    %input = '';
-    print "\n";
-    last;
-    }
-    elsif ( $_ =~ /^parse2/ ) {
-    #print "parse2: $in, $in2, $values[1], $values[2], $values[3], $values[4], $values[5], %yml_hash, %yml_hash_arguments, $yml_hash, $yml_hash_arguments\n";
-    parse2 ($in, $in2, $values[1], $values[2], $values[3], $values[4], $values[5], %yml_hash, %yml_hash_arguments, $yml_hash, $yml_hash_arguments);
-    print "parse2_out:$lookup...\n";
-    $test_command .= "$lookup";
-    $lookup = '';
-    $input = '';
-    %input = '';
-    print "\n";
-    last;
-    }
-    elsif ( $_ !~ /^parse1$/ && $_ !~ /^parse2$/ ) { print "$_ does not require matching!\n\n";
-    $test_command .= "$_";
-    last; 
-    }
-  }
-}
-
-print "\n";
-print "Resulting in following command: $test_command\n";
-system ($test_command);
-print "Job done program stopping.\n";
-
-#testing parse2
-#%in = $inyml;
-#$pattern1 = "PROTOCOL";
-#$pattern2 = "$inprotocol$inprotocolversion";
-#$pattern2 = "$inprotocol";
-#$pattern3 = "NAME";
-#$pattern4 = "ANALYSIS";
-#$pattern5 = "DATABASES";
-#parse2 ($in, $yml_hash_arguments, $pattern1, $pattern2, $pattern3, $pattern4, $pattern5);
-
-#application is checked as well
-#testing parse3
-#%in = $inyml;
-#$pattern1 = "OTHERINFO";
-#$pattern2 = $application; #is value is which used for check
-#patteern3 = "APPLICATION";
-#$pattern4 = "GENERAL";
-#parse1 ($in, $yml_hash_arguments, $pattern1, $pattern2, $pattern3, $pattern4);
-
-exit;
-
-#####################
-#!!!END OF SCRIPT!!!#
-####################
-
-#############
-#SUBROUTINES#
-#############
-
-sub check_lookup {
-if ($in_lookup =~ /^$/) {
-  #No argument found error, mismatch between arguments and inyml!
-  print " mismatch between yml input and arguments yml!\n";
-  print "Problem with following values: $in_key: $in_value!\n"; }  
-elsif ($in_lookup !~ /^$/) {
-  #argument found in arguments file!             
-  print " found argument!\n";
-  print "Following values used: $in_key:$in_value:$in_lookup!\n";
-  $match1++; }
-}
-
-#############
-#Subroutine to process parsing for 2-layered arrays in yamls
-#############
-sub parse2 { 
-
-#presetting variables
-$input = '';
-%input = '';
-$lookup = '';
-my $find_parameter;
-my $find_parameter_result;
-my $count_key;
-my $count_value;
-my $count_inner_key;
-my $count_inner_value;
-my %test_value_ANALYSIS;
-my %test_value_GENERAL;
-my $pattern1 = $_[2];
-my $pattern2 = $_[3];
-my $pattern3 = $_[4];
-my $pattern4 = $_[5];
-my $pattern5 = $_[6];
-
-print "Searching for matching parameter for: $pattern1...";
-
-for my $test_value_ANALYSIS (@{$yml_hash->{$pattern4}{$pattern5}}) {
-  $count_key = 0;
-  foreach my $key (keys $test_value_ANALYSIS) {
-    $count_key++;
-    $count_value = 1;
-    foreach my $value (values $test_value_ANALYSIS) {
-      if ($count_value =~ /^$count_key$/) { 
-        for my $test_value_ANALYSIS_arguments (@{$yml_hash_arguments->{$pattern4}{$pattern5}}) {
-          $count_inner_key = 0;
-          foreach my $inner_key (keys $test_value_ANALYSIS_arguments ) {
-            if ( $key =~ /^$inner_key$/ ) { 
-              $count_inner_key++;
-              $count_inner_value = 1;
-              foreach my $inner_value (values $test_value_ANALYSIS_arguments) {
-                $match1 = 0;
-                $lookup = "";
-                if ( $test_value_ANALYSIS_arguments->{$pattern3} =~ /^$pattern2$/ && $test_value_ANALYSIS->{$pattern3} =~ /^$pattern2$/ ) {
-                  if ( $count_inner_value =~ /^$count_inner_key$/ && $key =~ /^$pattern1$/) {
-                    if ( $test_value_ANALYSIS_arguments->{$key} =~ /^HASH/ ) {
-                      #print "\nIs hash! $key:$value:$inner_key:$inner_value:$pattern1\n";
-                      $lookup = $test_value_ANALYSIS_arguments->{$key}{$value};
-                      check_lookup ($in_key = $key,$in_value = $value, $in_lookup = $lookup, $match1);
-                      $in_key = '';
-                      $in_value = '';
-                      $in_lookup = '';
-                      return;
-                    }
-                    elsif ( $test_value_ANALYSIS_arguments->{$key} !~ /^HASH/ ) {
-                      $lookup = $test_value_ANALYSIS_arguments->{$key};
-                      check_lookup ($in_key = $key,$in_value = $value, $in_lookup = $lookup, $match1);
-                      $in_key = '';
-                      $in_value = '';
-                      $in_lookup = '';
-                      return; 
-                    }
-                  } 
-                $count_inner_value++;
-                }
-              }
-            }
-          }    
-        } 
-      }
-      $count_value++;
-    }
-  }
-}
-
-print " parameter not found!\n";
-print "Problem with following value: $pattern1!\n";
-print "Please check your yaml files for errors!\n";
-print "Aborting...\n";
-
-} 
-
-#############
-#Subroutine to process parsing of 1-layered array in yamls
-#############
-sub parse1 {
-
-#presetting variables
-%input = '';
-$lookup = '';
-my $find_parameter;
-my $find_parameter_result;
-my $count_key;
-my $count_value;
-my $count_inner_key;
-my $count_inner_value;
-my %test_value_ANALYSIS;
-my %test_value_GENERAL;
-my $pattern1 = $_[2];
-my $pattern2 = $_[3];
-my $pattern3 = $_[4];
-my $pattern4 = $_[5];
-
-print "Searching for matching parameter for: $pattern1...";
-
-foreach my $find_parameter (@{$yml_hash->{$pattern4}}) {
-  #print "hash: $find_parameter->{$pattern1}\n";
-}
-
-for my $test_value_ANALYSIS (@{$yml_hash->{$pattern4}}) {
-  $count_key = 0;
-  foreach my $key (keys $test_value_ANALYSIS) {
-    $count_key++;
-    $count_value = 0;
-    foreach my $value (values $test_value_ANALYSIS) {
-      $count_value++;
-      if ($count_value =~ /^$count_key$/) {
-        for my $test_value_ANALYSIS_arguments (@{$yml_hash_arguments->{$pattern4}}) {
-          $count_inner_key = 0;
-          foreach my $inner_key (keys $test_value_ANALYSIS_arguments ) {
-            $count_inner_key++;
-            $count_inner_value = 0;
-            if ( $key =~ /^$inner_key$/ ) {
-              foreach my $inner_value (values $test_value_ANALYSIS_arguments) {
-                $count_inner_value++;
-                #print "Innervalue: $inner_value $key:$value:$inner_key:$inner_value:$count_key:$count_value:$count_inner_key:$count_inner_value\n";
-                $match1 = 0;
-                $lookup = "";
-                if ( $test_value_ANALYSIS_arguments->{$pattern3} =~ /^$pattern2$/ && $test_value_ANALYSIS->{$pattern3} =~ /^$pattern2$/ ) {
-                  if ( $count_inner_value =~ /^$count_inner_key$/ && $key =~ /^$pattern1$/ ) {
-                    if ( $test_value_ANALYSIS_arguments->{$key} =~ /^HASH/ ) {
-                      #print "\nIs hash! $key:$value:$inner_key:$lookup:$match1\n";
-                      $lookup = $test_value_ANALYSIS_arguments->{$key}{$value};
-                      check_lookup ($in_key = $key,$in_value = $value, $in_lookup = $lookup, $match1);
-                      $in_key = '';
-                      $in_value = '';
-                      $in_lookup = '';
-                      return;
-                    }
-                    elsif ( $test_value_ANALYSIS_arguments->{$key} !~ /^HASH/ ) {
-                      $lookup = $test_value_ANALYSIS_arguments->{$key};
-                      #print "Is not a Hash! $lookup\n";
-                      check_lookup ($in_key = $key,$in_value = $value, $in_lookup = $lookup, $match1);
-                      $in_key = '';
-                      $in_value = '';
-                      $in_lookup = ''; 
-                      return;
-                    }
-                  }
-                }
-              }
-            }
-          }
-        }
-      }
-    }
-  }
-}
-
-print " parameter not found!\n";
-print "Problem with following value: $pattern1!\n";
-print "Please check your yaml files for errors!\n";
-print "Aborting...\n";
-
-} 
-
-#############
-#subroutine parsing yaml hash
-#############
-sub openyml_write {
-my $outyml = $in; 
-#Create second yml file with change values originating from cli
-open(OUT, '>', "$outyml") or die "Could not open file '$outyml' $!";
-print "Done creating output file...\n";
-}
-
-#############
-#
-#############
-sub openyml_read { 
-$in = $_[0];
-chomp $in;
-my $inyml = $in;
-open(FILE, '<', "$inyml") or die "Could not open file '$inyml' $!";
-close FILE;
-print "Done reading\n";
-}
-
-#############
-##
-##############
-sub load_arguments {
-$in = $_[0];
-$yml_hash_arguments = LoadFile($in);
-return($yml_hash_arguments, %yml_hash_arguments);
-}
-
-#############
-#pen(FILE, '<', "$inyml") or die "Could not open file '$inyml' $!";
-##
-##############
-sub load {
-$in = $_[0];
-$yml_hash = LoadFile($in);
-return($yml_hash, %yml_hash);
-}
-
-#############
-##
-##############
-sub load_edit {
-$in = $_[0];
-$yml_hash_edit = LoadFile($in);
-}
-
-#############
-##
-##############
-sub writeyml {
-my $yml_hash = $in;
-$writer = sub {
-    my $line = shift;
-    print FILE "$line\n";
-};
-my $file = Data::YAML::Writer->new;
-$file->write( $yml_hash, $writer );
-}
-
-#############
-##
-##############
-sub writeyml_edit {
-my $yml_hash = $in;
-$writer = sub {
-    my $line = shift;
-    print OUT "$line\n";
-};
-my $file = Data::YAML::Writer->new;
-$file->write( $yml_hash_edit, $writer );
-close OUT;
-}
-
-#############
-##
-##############
-sub parse {
-my $ymlhash = $in;
-
-print "searching for: $pattern\n";
-
-$match = "0";
-$match_value = '';
-
-for my $key1 (keys %{$yml_hash}) {
-#print "Key1: $key1\n";
-$type = '';
-$type = ref(${$yml_hash}{$key1});
-    if (exists $yml_hash->{$key1} || $type =~ /HASH/) {
-        for my $key2 (keys %{$yml_hash->{$key1}}) {
-        #print "Key2: $key2\n";
-        $type = '';
-        $type = ref(${$yml_hash}{$key1}{$key2});
-            if (exists $yml_hash->{$key2} || $type =~ /HASH/) {
-                for my $key3 (keys %{$yml_hash->{$key1}{$key2}}) {
-                #print "Key3: $key3\n";
-                $type = '';
-                $type = ref(${$yml_hash}{$key1}{$key2}{$key3});
-                    if (exists $yml_hash->{$key3} || $type =~ /HASH/) {
-                        for my $key4 (keys %{$yml_hash->{$key1}{$key2}{$key3}}) {
-                        #print "Key4: $key4\n";
-                        $type = '';
-                        $type = ref(${$yml_hash}{$key1}{$key2}{$key3}{$key4});
-                            if (exists $yml_hash->{$key4} || $type =~ /HASH/) {
-                                for my $key5 (keys %{$yml_hash->{$key1}{$key2}{$key3}{$key4}}) {
-                                #print "Key5: $key5\n";
-                                $type = '';
-                                $type = ref(${$yml_hash}{$key1}{$key2}{$key3}{$key4}{$key5});
-                                    if (exists $yml_hash->{$key5} || $type =~ /HASH/) {
-                                        for my $key6 (keys %{$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}}) {
-                                        #print "Key6: $key6\n";
-                                        $type = '';
-                                        $type = ref(${$yml_hash}{$key1}{$key2}{$key3}{$key4}{$key5}{$key6});
-                                            if (exists $yml_hash->{$key6} || $type =~ /HASH/) {
-                                                for my $key7 (keys %{$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}}) {
-                                                #print "Key7: $key7\n";
-                                                $type = '';
-                                                $type = ref(${$yml_hash}{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7});
-                                                    if (exists $yml_hash->{$key7} || $type =~ /HASH/) {
-                                                        for my $key8 (keys %{$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}}) {
-                                                        #print "Key8: $key8\n";
-							$type = '';
-							$type = ref(${$yml_hash}{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8});
-							    if (exists $yml_hash->{$key8} || $type =~ /HASH/) {
-							        for my $key9 (keys %{$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}}) {
-								#print "Key9: $key9\n";
-								$type = '';
-								$type = ref(${$yml_hash}{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}{$key9});
-                                                                    if (exists $yml_hash->{$key9} || $type =~ /HASH/) {
-									for my $key10 (keys %{$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}{$key9}}) {
-									my $value = "$key1:$key2:$key3:$key4:$key5:$key6:$key7:$key8:$key9 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}{$key9}{$key10}";
-									if ( $value =~ /$pattern/ ) {
-									    $match++;
-									    $match_value = "$key1:$key2:$key3:$key4:$key5:$key6:$key7:$key8:$key9:$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}{$key9}{$key10}";
-									    #print "value $key1:$key2:$key3:$key4:$key5:$key6:$key7:$key8:$key9 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}{$key9}{$key10}\n";
-									}
-									#print "$key1:$key2:$key3:$key4:$key5:$key6:$key7:$key8:$key9 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}{$key9}{$key10}";
-								    }		
-								} else {	
-								my $value = "$key1:$key2:$key3:$key4:$key5:$key6:$key7:$key8:$key9 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}{$key9}";
-							        if ( $value =~ /$pattern/ ) {
-								    $match++;
-								    $match_value = "$key1:$key2:$key3:$key4:$key5:$key6:$key7:$key8:$key9:$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}{$key9}";
-								    #print "value: $key1:$key2:$key3:$key4:$key5:$key6:$key7:$key8:$key9 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}{$key9}\n";
-								} 
-								#print "value: $key1:$key2:$key3:$key4:$key5:$key6:$key7:$key8:$key9 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}{$key9}\n";
-								}
-							    }
-							} else {
-							my $value = "$key1:$key2:$key3:$key4:$key5:$key6:$key7:$key8 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}";
-							if ( $value =~ /$pattern/ ) {
-                                                            $match++;
-							    $match_value =  "$key1:$key2:$key3:$key4:$key5:$key6:$key7:$key8:$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}";
-                                                            #print "value: $key1:$key2:$key3:$key4:$key5:$key6:$key7:$key8 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}\n";
-							}
-							#print "value: $key1:$key2:$key3:$key4:$key5:$key6:$key7:$key8 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}{$key8}\n";
-                                                        }
-						    }
-                                                } else {
-						my $value = "$key1:$key2:$key3:$key4:$key5:$key6:$key7 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}";
-						if ( $value =~ /$pattern/ ) {
-						    $match++;
-						    $match_value = "$key1:$key2:$key3:$key4:$key5:$key6:$key7:$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}";
-                                                    #print "value: $key1:$key2:$key3:$key4:$key5:$key6:$key7 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}\n";
-						}
-						#print "value: $key1:$key2:$key3:$key4:$key5:$key6:$key7 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}{$key7}\n";
-                                                }
-                                             }
-                                         } else {
-					 my $value = "$key1:$key2:$key3:$key4:$key5:$key6 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}";
-					 if ( $value =~ /$pattern/ ) {
-					     $match++;
-					     $match_value = "$key1:$key2:$key3:$key4:$key5:$key6:$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}";
-                                             #print "value: $key1:$key2:$key3:$key4:$key5:$key6 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}\n";
-					 }
-					 #print "value: $key1:$key2:$key3:$key4:$key5:$key6 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}{$key6}\n";
-                                         }
-                                      }
-                                  } else {
-				  my $value = "$key1:$key2:$key3:$key4:$key5 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}";
-				  if ( $value =~ /$pattern/ ) {
-				      $match++;
-				      $match_value = "$key1:$key2:$key3:$key4:$key5:$yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}";
-                                      #print "value: $key1:$key2:$key3:$key4:$key5 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}\n";
-				  }
-				  #print "value: $key1:$key2:$key3:$key4:$key5 $yml_hash->{$key1}{$key2}{$key3}{$key4}{$key5}\n";
-                                  }
-                               }
-                           } else {
-			   my $value = "$key1:$key2:$key3:$key4 $yml_hash->{$key1}{$key2}{$key3}{$key4}";
-			   if ( $value =~ /$pattern/ ) {
-			       $match++;
-			       $match_value = "$key1:$key2:$key3:$key4:$yml_hash->{$key1}{$key2}{$key3}{$key4}";
-                               #print "value: $key1:$key2:$key3:$key4 $yml_hash->{$key1}{$key2}{$key3}{$key4}\n";
-			   }
-			   #print "value: $key1:$key2:$key3:$key4 $yml_hash->{$key1}{$key2}{$key3}{$key4}\n";
-                           }
-                        }
-                    } else {
-		    my $value = "$key1:$key2:$key3 $yml_hash->{$key1}{$key2}{$key3}";
-		    if ( $value =~ /$pattern/ ) {
-			$match++;
-			$match_value = "$key1:$key2:$key3:$yml_hash->{$key1}{$key2}{$key3}";
-                        #print "value: $key1:$key2:$key3 $yml_hash->{$key1}{$key2}{$key3}\n";
-		    }
-		    #print "value: $key1:$key2:$key3 $yml_hash->{$key1}{$key2}{$key3}\n";
-                    }
-                }
-            } else {
-	    my $value = "$key1:$key2 $yml_hash->{$key1}{$key2}";
-	    if ( $value =~ /$pattern/ ) {
-		$match++;
-		$match_value = "$key1:$key2:$yml_hash->{$key1}{$key2}";
-                #print "value: $key1:$key2 $yml_hash->{$key1}{$key2}\n";
-	    }
-	    #print "value: $key1:$key2 $yml_hash->{$key1}{$key2}\n";
-            }
-        }
-    } else {
-    my $value = "$key1 $yml_hash->{$key1}";
-    if ( $value =~ /$pattern/ ) {
-	$match++;
-	$match_value = "$key1:$yml_hash->{$key1}";
-        #print "value: $key1 $yml_hash->{$key1}\n";
-    }
-    #print "value: $key1 $yml_hash->{$key1}\n";
-    }
-}
-
-print "Match: $match\n";
-
-return $match;
-return $match_value;
-} 
--- a/annovar_yaml/annovar_yaml.xml	Tue May 14 05:07:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-<tool id="annovar_yaml" name="Annovar YAML" version="0.1.0">
-    <requirements>
-        <requirement type="package" version="5.22">perl</requirement>
-        <requirement type="package" version="1.27">perl-yaml</requirement>
-        <requirement type="package" version="1.73">perl-yaml-tiny</requirement>
-        <requirement type="package" version="0.74">perl-yaml-xs</requirement>
-        <requirement type="package" version="2.173">perl-data-dumper</requirement>
-        <requirement type="package" version="2.50">perl-getopt-long</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-        perl $__tool_directory__/annovar_yaml.pl --invcf $vcf --inyml $yaml --outvcf $output
-    ]]></command>
-
-    <inputs>
-
-        <param type="data" name="yaml" format="txt" />
-        <param type="data" name="vcf" format="vcf" />
-
-    </inputs>
-    <outputs>
-        <data name="output" format="vcf"/>
-    </outputs>
-    <help><![CDATA[
-        TODO: Fill in help for Annovar YAML tool. perl 5.22
-    ]]></help>
-</tool>