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scripts/bam2wig.pl  view on Meta::CPAN

# Command line options
GetOptions(
	'i|in=s'            => \@bamfiles,           # one or more bam files
	'o|out=s'           => \$outfile,            # name of output file
	's|start!'          => \$use_start,          # record start point
	'd|mid!'            => \$use_mid,            # record mid point
	'a|span!'           => \$use_span,           # record span
	'cspan!'            => \$use_cspan,          # record center span
	'e|extend!'         => \$use_extend,         # extend read
	'smartcov!'         => \$use_smartpe,        # smart paired coverage
	'ends!'             => \$use_ends,           # record paired-end endpoints
	'coverage!'         => \$use_coverage,       # calculate coverage
	'position=s'        => \$position,           # legacy option
	'l|splice|split!'   => \$splice,             # split splices
	'p|pe!'             => \$paired,             # paired-end alignments
	'P|fastpe!'         => \$fastpaired,         # fast paired-end alignments
	'I|shift!'          => \$shift,              # shift coordinates 3'
	'H|shiftval=i'      => \$shift_value,        # value to shift coordinates
	'x|extval=i'        => \$extend_value,       # value to extend reads
	'chrom=i'           => \$chr_number,         # number of chromosomes to sample
	'minr=f'            => \$correlation_min,    # R minimum value for shift