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1 #!/usr/bin/perl -w
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2 #
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3 # Copyright (C) 2013 Genome Research Ltd.
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4 #
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5 # Author: James Bonfield <jkb@sanger.ac.uk>
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6 #
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7 # Permission is hereby granted, free of charge, to any person obtaining a copy
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8 # of this software and associated documentation files (the "Software"), to deal
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9 # in the Software without restriction, including without limitation the rights
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10 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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11 # copies of the Software, and to permit persons to whom the Software is
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12 # furnished to do so, subject to the following conditions:
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13 #
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14 # The above copyright notice and this permission notice shall be included in
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15 # all copies or substantial portions of the Software.
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16 #
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17 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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18 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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19 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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20 # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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21 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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22 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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23 # DEALINGS IN THE SOFTWARE.
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24
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25 # Compares two SAM files to report differences.
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26 # Optionally can skip header or ignore specific types of diff.
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27
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28 use strict;
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29 use Getopt::Long;
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30
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31 my %opts;
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32 GetOptions(\%opts, 'noqual', 'noaux', 'notemplate', 'unknownrg', 'nomd', 'template-1', 'noflag');
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33
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34 my ($fn1, $fn2) = @ARGV;
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35 open(my $fd1, "<", $fn1) || die $!;
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36 open(my $fd2, "<", $fn2) || die $!;
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37
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38 # Headers
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39 my ($c1,$c2)=(1,1);
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40 my (@hd1, @hd2, $ln1, $ln2);
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41 while (<$fd1>) {
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42 if (/^@/) {
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43 push(@hd1, $_);
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44 } else {
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45 $ln1 = $_;
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46 last;
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47 }
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48 $c1++;
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49 }
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50
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51 while (<$fd2>) {
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52 if (/^@/) {
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53 push(@hd2, $_);
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54 } else {
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55 $ln2 = $_;
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56 last;
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57 }
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58 $c2++;
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59 }
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60
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61 # FIXME: to do
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62 #print "@hd1\n";
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63 #print "@hd2\n";
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64
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65 # Compare lines
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66 while ($ln1 && $ln2) {
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67 chomp($ln1);
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68 chomp($ln2);
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69
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70 # Java CRAM adds RG:Z:UNKNOWN when the read-group is absent
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71 if (exists $opts{unknownrg}) {
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72 $ln1 =~ s/\tRG:Z:UNKNOWN//;
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73 $ln2 =~ s/\tRG:Z:UNKNOWN//;
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74 }
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75
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76 if (exists $opts{nomd}) {
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77 $ln1 =~ s/\tMD:Z:[A-Z0-9^]*//;
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78 $ln2 =~ s/\tMD:Z:[A-Z0-9^]*//;
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79 $ln1 =~ s/\tNM:i:\d+//;
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80 $ln2 =~ s/\tNM:i:\d+//;
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81 }
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82
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83 my @ln1 = split("\t", $ln1);
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84 my @ln2 = split("\t", $ln2);
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85
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86 # Fix BWA bug: unmapped data should have no alignments
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87 if ($ln1[1] & 4) { $ln1[4] = 0; $ln1[5] = "*"; }
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88 if ($ln2[1] & 4) { $ln2[4] = 0; $ln2[5] = "*"; }
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89
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90 # Rationalise order of auxiliary fields
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91 if (exists $opts{noaux}) {
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92 @ln1 = @ln1[0..10];
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93 @ln2 = @ln2[0..10];
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94 } else {
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95 #my @a=@ln1[11..$#ln1];print "<<<@a>>>\n";
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96 @ln1[11..$#ln1] = sort @ln1[11..$#ln1];
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97 @ln2[11..$#ln2] = sort @ln2[11..$#ln2];
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98 }
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99
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100 if (exists $opts{noqual}) {
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101 $ln1[10] = "*";
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102 $ln2[10] = "*";
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103 }
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104
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105 if (exists $opts{notemplate}) {
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106 @ln1[6..8] = qw/* 0 0/;
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107 @ln2[6..8] = qw/* 0 0/;
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108 }
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109
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110 if (exists $opts{noflag}) {
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111 $ln1[1] = 0; $ln2[1] = 0;
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112 }
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113
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114 if (exists $opts{'template-1'}) {
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115 if (abs($ln1[8] - $ln2[8]) == 1) {
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116 $ln1[8] = $ln2[8];
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117 }
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118 }
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119
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120 # Cram doesn't uppercase the reference
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121 $ln1[9] = uc($ln1[9]);
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122 $ln2[9] = uc($ln2[9]);
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123
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124 # Cram will populate a sequence string that starts as "*"
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125 $ln2[9] = "*" if ($ln1[9] eq "*");
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126
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127 # Fix 0<op> cigar fields
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128 $ln1[5] =~ s/(\D|^)0\D/$1/g;
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129 $ln1[5] =~ s/^$/*/g;
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130 $ln2[5] =~ s/(\D|^)0\D/$1/g;
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131 $ln2[5] =~ s/^$/*/g;
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132
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133 # Fix 10M10M cigar to 20M
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134 $ln1[5] =~ s/(\d+)(\D)(\d+)(\2)/$1+$3.$2/e;
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135 $ln2[5] =~ s/(\d+)(\D)(\d+)(\2)/$1+$3.$2/e;
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136
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137 if ("@ln1" ne "@ln2") {
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138 print "Diff at lines $fn1:$c1, $fn2:$c2\n";
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139 my @s1 = split("","@ln1");
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140 my @s2 = split("","@ln2");
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141 my $ptr = "";
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142 for (my $i=0; $i < $#s1; $i++) {
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143 if ($s1[$i] eq $s2[$i]) {
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144 $ptr .= "-";
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145 } else {
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146 last;
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147 }
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148 }
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149 print "1\t@ln1\n2\t@ln2\n\t$ptr^\n\n";
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150 exit(1);
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151 }
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152
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153 $ln1 = <$fd1>;
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154 $ln2 = <$fd2>;
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155
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156 $c1++; $c2++;
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157 }
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158
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159 if (defined($ln1)) {
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160 print "EOF on $fn1\n";
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161 exit(1);
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162 }
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163
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164 if (defined($ln2)) {
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165 print "EOF on $fn2\n";
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166 exit(1);
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167 }
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168
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169 close($fd1);
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170 close($fd2);
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171
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172 exit(0);
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