App::Fasops::Common - collection of common subroutines
use App::Fasops::Common; my $length = App::Fasops::Common::seq_length("AGCTTT---CCA");
my $chr_pos = App::Fasops::Common::align_to_chr( $intspan, $pos, $chr_start, $chr_strand, ); my $chr_pos = App::Fasops::Common::align_to_chr( $intspan, $pos, $chr_start, );
Give a chr position, return an align position starting from '1'.
my $pos = App::Fasops::Common::align_to_chr( $intspan, $chr_pos, $chr_start, $chr_strand, ); my $pos = App::Fasops::Common::align_to_chr( $intspan, $chr_pos, $chr_start, );
Give a chr position, return an align position starting from '1'. If the position in target is located in a gap, then return the left base's position. 5' for positive strand and 3' for negative stran. (Just like GATK's indel left align.)
my ( $r, $dprime ) = App::Fasops::Common::calc_ld("111000", "111000");
Returns the r and D' (Hill and Robertson, 1968) of two polymorphic sites.
https://cran.r-project.org/web/packages/genetics/genetics.pdf
To install App::Fasops, copy and paste the appropriate command in to your terminal.
cpanm
cpanm App::Fasops
CPAN shell
perl -MCPAN -e shell install App::Fasops
For more information on module installation, please visit the detailed CPAN module installation guide.