App-Sandy

 view release on metacpan or  search on metacpan

lib/App/Sandy/DB/Handle/Variation.pm  view on Meta::CPAN

			unless $fields[5] =~ /^(HE|HO)$/;

		if ($fields[3] eq $fields[4]) {
			warn "There is an alteration equal to the reference at '$variation_file' line $line. I will ignore it\n";
			next;
		}

		# Sequence inside perl begins at 0
		my $position = int($fields[1] - 1);

		# Compare the alterations and reference to guess the max variation on sequence
		my $size_of_variation = max map { length } $fields[3], $fields[4];
		my $high = $position + $size_of_variation - 1;

		my %variation = (
			seq_id => $fields[0],
			id     => $fields[2],
			ref    => $fields[3],
			alt    => $fields[4],
			plo    => $fields[5],
			pos    => $position,

lib/App/Sandy/DB/Handle/Variation.pm  view on Meta::CPAN

			my $i = $g1 > $g2
				? $g1 - 1
				: $g2 - 1;
			$alternate = $alternates[$i];
			$plo = 'HE';
		}

		# Sequence inside perl begins at 0
		my $position = int($fields[1] - 1);

		# Compare the alterations and reference to guess the max variation on sequence
		my $size_of_variation = max map { length } $fields[3], $alternate;
		my $high = $position + $size_of_variation - 1;

		my %variation = (
			seq_id => $fields[0],
			id     => $fields[2],
			ref    => $fields[3],
			alt    => $alternate,
			plo    => $plo,
			pos    => $position,

lib/App/Sandy/Role/Digest.pm  view on Meta::CPAN

	$opts->{'id'} .= " $opts->{'append-id'}" if defined $opts->{'append-id'};

	# If bam, leave only the first field;
	if ($opts->{'output-format'} =~ /^(bam|sam)$/) {
		$opts->{'id'} = (split ' ' => $opts->{'id'})[0];
	}

	# In this case, try to make simulation less redundant
	if ($opts->{'output-format'} =~ /fastq/ && $opts->{'sequencing-type'} eq 'paired-end'
		&& $opts->{'join-paired-ends'}) {
		# Try to guess if the user passed a char to distinguish single/paired-end reads
		$opts->{'id'} =~ /%R/ || $opts->{'id'} =~ s/(\S+)/$1\/\%R/;
	}

	# Structural Variation
	if ($opts->{'genomic-variation'}) {
		my @svs = split(/,/ => join(',', @{ $opts->{'genomic-variation'} }));
		@svs = uniq sort @svs;
		$opts->{'genomic-variation'} = \@svs;
	}

ppport.h  view on Meta::CPAN

                      "help by submitting a documentation patch";
            }
            print ".\n";
            if ($todo) {
                if ($todo <= $int_min_perl) {
                    print "It may very well be supported all the way back to ",
                          format_version(5.003_07), ".\n";
                }
                else {
                    print "But given the things $f depends on, it's a good",
                          " guess that it isn't\n",
                          "supported prior to ", format_version($todo), ".\n";
                }
            }
        }
    }
    if ($API{$f}{provided}) {
      print "Support needs to be explicitly requested by #define NEED_$f\n",
            "(or #define NEED_${f}_GLOBAL).\n"              if exists $need{$f};
      $info++;
    }

ppport.h  view on Meta::CPAN

#ifndef UV_MAX
#  define UV_MAX                         PERL_ULONG_MAX
#endif

#endif

#ifndef IVSIZE
#  ifdef LONGSIZE
#    define IVSIZE LONGSIZE
#  else
#    define IVSIZE 4 /* A bold guess, but the best we can make. */
#  endif
#endif
#ifndef UVTYPE
#  define UVTYPE                         unsigned IVTYPE
#endif

#ifndef UVSIZE
#  define UVSIZE                         IVSIZE
#endif