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2 =head1 LICENSE
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3
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4 Strelka Workflow Software
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5 Copyright (c) 2009-2013 Illumina, Inc.
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6
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7 This software is provided under the terms and conditions of the
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8 Illumina Open Source Software License 1.
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9
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10 You should have received a copy of the Illumina Open Source
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11 Software License 1 along with this program. If not, see
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12 <https://github.com/downloads/sequencing/licenses/>.
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13
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14 =cut
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15
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16
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17 package Utils;
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18
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19 use base 'Exporter';
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20
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21 our @EXPORT = qw(
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22 errorX logX executeCmd checkFile checkDir checkMove
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23 getAbsPath checkMakeDir getBinList
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24 parseConfigIni writeConfigIni
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25 );
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26
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27 use warnings FATAL => 'all';
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28 use strict;
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29
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30 use Carp;
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31 use Cwd qw(realpath);
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32 use File::Copy qw(move);
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33 use File::Path qw(mkpath);
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34
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35
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36 sub errorX($) {
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37 confess "\nERROR: " . $_[0] . "\n\n";
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38 }
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39
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40 sub logX($) {
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41 print STDERR "INFO: " . $_[0] . "\n";
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42 }
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43
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44
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45 sub executeCmd($;$) {
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46 my $cmd = shift;
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47 my $isVerbose = shift;
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48
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49 logX("Running: '$cmd'") if(defined($isVerbose) and $isVerbose);
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50 system($cmd) == 0
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51 or errorX("Failed system call: '$cmd'");
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52 }
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53 #return an error if file does not exist
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54 sub checkFile($;$) {
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55 my $file = shift;
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56 return if(-f $file);
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57 my $label = shift;
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58 errorX("Can't find" . (defined($label) ? " $label" : "") . " file: '$file'");
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59 }
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60 #return an error if file does not Exist
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61 sub checkDir($;$) {
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62 my $dir = shift;
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63 return if(-d $dir);
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64 my $label = shift;
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65 errorX("Can't find" . (defined($label) ? " $label" : "") . " directory: '$dir'");
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66 }
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67
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68 sub checkMove($$) {
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69 my ($old,$new) = @_;
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70 move($old,$new) || errorX("File move failed: $!\n\tAttempting to move '$old' to '$new'");
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71 }
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72
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73
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74
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75
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76 =item getAbsPath($path)
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77
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78 This procedure attempts to convert a path provided by the user on the
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79 command line into an absolute path. It should be able to handle "~"
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80 paths and conventional relative paths using ".." or ".". Resolution of
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81 links should follow the convention of "Cwd::realpath".
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82
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83 B<Parameters:>
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84
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85 $dirRef - path (converted to absolute path in place)
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86
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87 B<Returns:>
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88
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89 returns zero if successful, non-zero otherwise.
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90
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91 =cut
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92 sub getAbsPath(\$) {
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93 my ($dirRef) = @_;
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94 my @tmp=glob($$dirRef);
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95 return 1 if(scalar(@tmp) != 1);
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96 my $ret = Cwd::realpath($tmp[0]);
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97 return 1 if !$ret && !($ret = File::Spec->rel2abs($tmp[0]));
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98 $$dirRef = $ret;
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99 return 0;
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100 }
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101
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102
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103 #verify path is not a file, then create a directory with this name if does not exist
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104 sub checkMakeDir($) {
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105 my $dir = shift;
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106 unless (-e $dir) {
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107 File::Path::mkpath($dir) || errorX("Can't create directory '$dir'");
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108 } else {
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109 errorX("Path is not a directory '$dir'\n") unless(-d $dir);
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110 }
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111 }
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112
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113
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114
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115 sub getBinList($$) {
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116 my ($chromSize,$binSize) = @_;
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117
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118 my $nm1 = (($chromSize-1) / $binSize);
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119 return [ map {sprintf("%04i",$_)} (0..$nm1) ];
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120 }
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121
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122
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123
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124 sub parseConfigError($$) {
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125 my ($file,$line) = @_;
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126 errorX("Config file '$file' contains unexpected line '$line'\n");
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127 }
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128
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129 #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 $section=user).
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130 sub parseConfigIni($) {
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131 my $file = shift;
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132 my %config;
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133 open(my $FH,"< $file") || errorX("Can't open config file '$file'");
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134 my $section = "noSection";
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135 while(<$FH>) {
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136 next if(/^[;#]/);
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137 next if(/^\s*$/);
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138 chomp;
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139 my $line=$_;
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140 my @ncl = split(/[;#]/);
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141 next unless(scalar(@ncl));
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142 my $nc = $ncl[0];
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143 if($nc =~ /^\s*\[([^\]]*)\]\s*$/) {
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144 $section = $1;
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145 next;
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146 }
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147 my ($key,$val) = map { s/^\s+//; s/\s+$//; $_ } split(/=/,$nc,2);
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148 unless(defined($key) && defined($val) && ($key ne "")) { parseConfigError($file,$line); }
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149
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150 $config{$section}{$key} = $val;
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151 }
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152 close($FH);
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153 return \%config;
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154 }
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155
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156
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157 # minimal ini stringifier:
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158 #
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159 sub writeConfigIni($) {
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160 my $config = shift;
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161 my $val = "";
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162 for my $section (sort(keys(%$config))) {
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163 $val .= "\n[$section]\n";
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164 for my $key (sort(keys(%{$config->{$section}}))) {
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165 $val .= "$key = " . $config->{$section}{$key} . "\n";
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166 }
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167 }
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168 return $val;
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169 }
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170
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171
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172 1;
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