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MaveDB: only keep the columns and records that can be used #853

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MaveDB: only keep the columns and records that can be used #853

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26 changes: 25 additions & 1 deletion MaveDB.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -128,6 +128,24 @@ sub _parse_colnames {
}
}

sub _set_parsed_columns {
my $self = shift;

# The columns parse_data keeps per record: the ones we print, plus the two run() reads directly -
# and those only when the option that consults them is on. Data files carry a few hundred columns,
# so building a hash of all of them per record costs gigabytes at a locus with many records in a
# variant's span, whatever the user asked to print.
my %keep = map { $_ => 1 } @{ $self->{cols} };
$keep{"MaveDB_hgvs"} = 1 if $self->{single_aa_changes};
$keep{"MaveDB_refseq"} = 1 if $self->{transcript_match};

my $colnames = $self->{colnames};
my @indexes = grep { $keep{ $colnames->[$_] } } 0 .. scalar(@$colnames) - 1;

$self->{parsed_col_indexes} = \@indexes;
$self->{parsed_colnames} = [ map { $colnames->[$_] } @indexes ];
}

sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
Expand All @@ -152,6 +170,7 @@ sub new {
# Parse column names
my $cols = $param_hash->{cols} || "urn:score:nt:pro:doi";
$self->_parse_colnames($cols);
$self->_set_parsed_columns();

return $self;
}
Expand Down Expand Up @@ -308,6 +327,11 @@ sub parse_data {
my ($self, $line) = @_;
my ($chrom, $start, $end, $ref, $alt, @vals) = split /\t/, $line;

# Score sets mapped through VRS carry a "ga4gh:VA.<digest>" identifier in place of the reference
# sequence. get_matched_variant_alleles compares alleles as strings, so those records can never
# match anything - skip them rather than holding them in memory for the length of the buffer.
return undef if $ref =~ /^ga4gh:/;

# VCF-like adjustment of mismatched substitutions for comparison with VEP
if(length($alt) != length($ref)) {
my $first_ref = substr($ref, 0, 1);
Expand All @@ -322,7 +346,7 @@ sub parse_data {
}

my %res;
@res{ @{ $self->{colnames} } } = @vals;
@res{ @{ $self->{parsed_colnames} } } = @vals[ @{ $self->{parsed_col_indexes} } ];

return {
ref => $ref,
Expand Down