Sanger::CGP::TraFiC::Parser
use Sanger::CGP::TraFiC::Parser; my $parser = Sanger::CGP::TraFiC::Parser->new; $parser->set_output('output/folder); $parser->process_files($list_of_bams);
Only one end of the pair was mapped
Both ends of pair where mapped to different chromosomes
Both ends mapped to same chromosome but not as a proper pair (i.e. intRA chromosomal)
Set the root path that output should be sent to. Generates file-handles to the 6 files required for processing.
$parser->set_output('/some/existing/path');
Find and output candidate reads in the supplied files.
$parser->process_files([filelist, ...]); or $parser->process_files([singlefile], readgroup_id);
When readgroup_id is supplied only reads within the group will be handled. Using this inappropriately will result in no output for files that don't have the specified group. There will be no warnings when this occurs.
Takes a pair of reads and determines if they are suitable for processing as aberrant.
my ($class, $detail, $fasta) = $parser->pair_to_candidate($sam_r1, $sam_r2); next unless(defined $class);
\@ of the following values
$class : Type of aberrant read FastA record (see L</Constants>) $fasta : FastA record ready for printing
When the pair of reads input into this function are not found to be candidates an empty array ref is returned.