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Fix get_end VCF parser - ENSINT-2005 #171

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merged 4 commits into from
Nov 8, 2024
Merged

Fix get_end VCF parser - ENSINT-2005 #171

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072bcc5
Fix get_end VCF parser - ENSINT-2005
sgiorgetti Oct 8, 2024
edfad27
Update modules/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm
sgiorgetti Oct 28, 2024
3299c7a
Fix - added missing variable declaration
sgiorgetti Oct 28, 2024
d36e0b7
Fix - VCF parser - get_end
sgiorgetti Oct 29, 2024
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5 changes: 2 additions & 3 deletions modules/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -316,11 +316,10 @@ sub get_end {
elsif(defined($info->{SVLEN})) {
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@nakib103 nakib103 Oct 29, 2024 •
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@sgiorgetti,

Regarding - https://github.com/Ensembl/ensembl-io/pull/171/files#r1814776276

  1. The expected change would be to change the order in the if-elsif like so,

currently we have -

    if (defined($info->{END})) {
      $end = $info->{END};
    }
    elsif(defined($info->{SVLEN})) {
      return unless $self->get_start;
      my $svlen = (split(',',$info->{SVLEN}))[0];
      $end = $self->get_start + abs($svlen) - 1;
    }

change it to -

    if (defined($info->{SVLEN})) {
      return unless $self->get_start;
      my $svlen = (split(',',$info->{SVLEN}))[0];
      $end = $self->get_start + abs($svlen) - 1;
    }
    elsif (defined($info->{END})) {
      $end = $info->{END};
    }

So we calculate end using SVLEN first if available.

  1. Also, for sub get_raw_end, it is better to change it to call get_end as all these changes should be added in get_raw_end too (but we do not want to duplicate effort) -
sub get_raw_end {
    my $self = shift;
    return $self->get_end;
}

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Yes ... and you mentioned that before ... bear with me

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thanks @sgiorgetti !

return unless $self->get_start;
my $svlen = (split(',',$info->{SVLEN}))[0];
$end = $self->get_start + abs($svlen)-1;
$end = $self->get_start + abs($svlen) - 1;
}
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else {
return unless $self->get_start;
$end = $self->get_start + length($self->get_raw_reference) - 1;
$end = $self->get_raw_start + length($self->get_raw_reference) - 1;
}
return $end;
}
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1 change: 1 addition & 0 deletions modules/t/input/data.vcf
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Expand Up @@ -22,5 +22,6 @@
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 186302389 . TTA T 6 PASS . . . . .
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
20 1234567 INS0 C <ctg1> 6 PASS . . . . .
47 changes: 36 additions & 11 deletions modules/t/vcf.t
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ is_deeply($parser->{'record'},\@test_row,"Test basic parsing of a row");
note "> Testing each column of the row";
do_the_tests(\@test_row);
my $index = 0;
$test_sample = [$inds[$index], $test_row[9]];
$test_sample = [$inds[$index], $test_row[9+$index]];
$ind_info = $parser->get_raw_individuals_info($inds[$index]);
is_deeply($test_sample, $ind_info->[$index], 'Individual data (DEPRECATED)');
$sample_info = $parser->get_raw_samples_info($inds[$index]);
Expand All @@ -49,7 +49,7 @@ is_deeply($parser->{'record'},\@test_row,"Test basic parsing of a row");
note "> Testing each column of the row";
do_the_tests(\@test_row);
$index = 1;
$test_sample = [$inds[$index], $test_row[10]];
$test_sample = [$inds[$index], $test_row[9+$index]];
$ind_info = $parser->get_raw_individuals_info($inds[$index]);
is_deeply($test_sample, $ind_info->[$index], 'Individual data (DEPRECATED)');
$sample_info = $parser->get_raw_samples_info($inds[$index]);
Expand All @@ -63,7 +63,7 @@ is_deeply($parser->{'record'},\@test_row,"Test basic parsing of a row");
note "> Testing each column of the row";
do_the_tests(\@test_row);
$index = 2;
$test_sample = [$inds[$index], $test_row[11]];
$test_sample = [$inds[$index], $test_row[9+$index]];
$ind_info = $parser->get_raw_individuals_info($inds[$index]);
is_deeply($test_sample, $ind_info->[$index], 'Individual data (DEPRECATED)');
$sample_info = $parser->get_raw_samples_info($inds[$index]);
Expand All @@ -77,30 +77,41 @@ is_deeply($parser->{'record'},\@test_row,"Test basic parsing of a row");
note "> Testing each column of the row";
do_the_tests(\@test_row);
$index = 0;
$test_sample = [$inds[$index], $test_row[9]];
$test_sample = [$inds[$index], $test_row[9+$index]];
$ind_info = $parser->get_raw_individuals_info($inds[$index]);
is_deeply($test_sample, $ind_info->[$index], 'Individual data (DEPRECATED)');
$sample_info = $parser->get_raw_samples_info($inds[$index]);
is_deeply($test_sample, $sample_info->[$index], 'Sample data');


note "Record 5";
ok ($parser->next(), "Loading fifth record");
ok ($parser->next(), "Loading the fifth record");
@test_row = (qw(20 186302389 . TTA T 6 PASS . . . . .));
is_deeply($parser->{'record'},\@test_row,"Test basic parsing of a row");
note "> Testing each column of the row";
do_the_tests(\@test_row);
ok($parser->get_seqname eq '20', 'get_seqname');
ok($parser->get_start == 186302390, 'get_start');
ok($parser->get_end == 186302391, 'get_end');


note "Record 6";
ok ($parser->next(), "Loading the sixth record");
@test_row = (qw(20 1234567 microsat1 GTC), 'G,GTCT', 50, 'PASS', qw(NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3));
is_deeply($parser->{'record'},\@test_row,"Test basic parsing of a row");
note "> Testing each column of the row";
do_the_tests(\@test_row);
$index = 0;
$test_sample = [$inds[$index], $test_row[9]];
$index = 1;
$test_sample = [$inds[$index], $test_row[9+$index]];
$ind_info = $parser->get_raw_individuals_info($inds[$index]);
is_deeply($test_sample, $ind_info->[$index], 'Individual data (DEPRECATED)');
$sample_info = $parser->get_raw_samples_info($inds[$index]);
is_deeply($test_sample, $sample_info->[$index], 'Sample data');

print "\n> Testing the getters (only for the last record):\n";
print "> Testing the getters (only for the 6th record):\n";
ok($parser->get_seqname eq '20', 'get_seqname');
ok($parser->get_start == 1234568, 'get_start');
ok($parser->get_end == 1234570, 'get_end');
ok($parser->get_end == 1234569, 'get_end');
ok($parser->get_IDs->[0] eq 'microsat1', 'get_IDs');
ok($parser->get_reference eq 'GTC', 'get_reference');
ok($parser->get_alternatives->[0] eq 'G', 'get_alternatives');
Expand All @@ -116,7 +127,21 @@ ok($parser->get_individuals_genotypes($inds[$index])->{$inds[$index]} eq 'GTC/G'
ok($parser->get_samples_info($inds[$index])->{$inds[$index]}->{'GT'} eq '0/1', 'get_samples_info');
ok($parser->get_samples_genotypes($inds[$index])->{$inds[$index]} eq 'GTC/G', 'get_samples_genotypes');

note "> Testing metadata getters";

note "Record 7";
ok ($parser->next(), "Loading the seventh record");
@test_row = (qw(20 1234567 INS0 C <ctg1> 6 PASS . . . . .));
is_deeply($parser->{'record'},\@test_row,"Test basic parsing of a row");
note "> Testing each column of the row";
do_the_tests(\@test_row);
$index = 2;
$test_sample = [$inds[$index], $test_row[9+$index]];
$ind_info = $parser->get_raw_individuals_info($inds[$index]);
is_deeply($test_sample, $ind_info->[$index], 'Individual data (DEPRECATED)');
$sample_info = $parser->get_raw_samples_info($inds[$index]);
is_deeply($test_sample, $sample_info->[$index], 'Sample data');

note "\n> Testing metadata getters";
ok($parser->get_metadata_key_list eq 'FILTER, FORMAT, INFO, contig, fileDate, fileformat, header, phasing, reference, source', 'getMetadataKeyList');
ok($parser->get_metadata_by_pragma('fileDate') eq '20090805', 'getMetadataByPragma');
ok($parser->get_vcf_version eq 'VCFv4.2', 'getVCFversion');
Expand All @@ -125,7 +150,7 @@ ok($parser->get_metadata_field('contig', '20', 'length') eq 62435964, 'getMetaFi
ok(!defined($parser->get_metadata_field('contig', '20', 'URL')), 'getMetaField - non-existing field');
ok($parser->get_metadata_field('contig', 'ctg1', 'URL') =~ /ftp/, 'Multiple contigs');

note "> Testing format validation";
note "\n> Testing format validation";
$parser->reset();
$parser->shift_block;
ok ($parser->validate(), "Validating vcf format");
Expand Down