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lib/App/Fasops/Common.pm  view on Meta::CPAN

#   T G----C
#   Q G----C
#   O GAAAAC
sub trim_outgroup {
    my $seq_refs = shift;

    my $seq_count = scalar @{$seq_refs};

    Carp::confess "Need three or more sequences\n" if $seq_count < 3;

    # Don't expand indel set here. Last seq is outgroup
    my @indel_intspans;
    for my $i ( 0 .. $seq_count - 2 ) {
        my $indel_intspan = indel_intspan( $seq_refs->[$i] );
        push @indel_intspans, $indel_intspan;
    }

    # find trim_region
    my $union_set     = AlignDB::IntSpan::union(@indel_intspans);
    my $intersect_set = AlignDB::IntSpan::intersect(@indel_intspans);

lib/App/Fasops/Common.pm  view on Meta::CPAN

#   Q G--C
#   O GGAC
sub trim_complex_indel {
    my $seq_refs = shift;

    my $seq_count   = scalar @{$seq_refs};
    my @ingroup_idx = ( 0 .. $seq_count - 2 );

    Carp::confess "Need three or more sequences\n" if $seq_count < 3;

    # Don't expand indel set here. Last seq is outgroup
    my @indel_intspans;
    for my $i (@ingroup_idx) {
        my $indel_intspan = indel_intspan( $seq_refs->[$i] );
        push @indel_intspans, $indel_intspan;
    }
    my $outgroup_indel_intspan = indel_intspan( $seq_refs->[ $seq_count - 1 ] );

    # find trim_region
    my $union_set     = AlignDB::IntSpan::union(@indel_intspans);
    my $intersect_set = AlignDB::IntSpan::intersect(@indel_intspans);