[ensembl-dev] Bio::EnsEMBL::Feature::strand doesn't match output strand in plugin

[Matt Wood]

I'm writing a plugin and am running into an issue with strand. The strand I
get from Bio::EnsEMBL::Feature::strand doesn't match the strand I'm seeing
in the output or the strand that is in the line hash provided to my run
method. Specifically I'm having an issue with the negative strand.

This is my test plugin:

package StrandTest;
use strict;
use warnings;
use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);

sub run {
    my ($self, $tva, $line_hash) = @_;

    my $strand = $tva->variation_feature->strand;
    my $extra_strand = $line_hash->{Extra}->{STRAND};

    print("Strand: $strand/$extra_strand\n");

    return {};
}

1;

My output shows this: "Strand: 1/-1"

The strand written to my output file is -1, and the strand in the line hash
is -1, but the strand from the VariationFeature is 1.

My VCF:

##fileformat=VCFv4.0
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    PAT
6    133078809    .    C    A    60    PASS    .    GT:VR:RR:DP:GQ
0/1:12:15:27:.

I'm running VEP with these options: --plugin StrandTest --offline --vcf
--force_overwrite --pick -i test.vcf -o test.vep

Any idea what's going on? For the time being I'm going to use
"$line_hash->{Extra}->{STRAND}" for my strand info. Is that safe to do? Are
there going to be cases where that hash is undef?

Thanks,
Matt Wood
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