Module: Bio::MAF

Defined in:
lib/bio/maf/parser.rb,
lib/bio/maf/maf.rb,
lib/bio/maf/jobs.rb,
lib/bio/maf/index.rb,
lib/bio/maf/tiler.rb,
lib/bio/maf/struct.rb,
lib/bio/maf/writer.rb

Defined Under Namespace

Modules: Executor, JobRunner, KVHelpers, MAFParsing Classes: Access, AllSpeciesFilter, AtLeastNSequencesFilter, BGZFChunkReader, Block, ChunkReader, CompletionTracker, DummyExecutor, DummyParser, EmptySequence, FASTARangeReader, FASTAWriter, Filter, Filters, ForkRunner, Header, JExecutor, JThreadRunner, KyotoIndex, MaxSizeFilter, Member, MinSizeFilter, ParseContext, ParseError, Parser, Sequence, Struct, ThreadedChunkReaderWrapper, Tiler, Writer

Constant Summary collapse

LOG = 
Bio::Log::LoggerPlus['bio-maf']
TYPE_PROPS = 
{
  :uint8  => { :size => 1, :fmt => 'C'  },
  :uint16 => { :size => 2, :fmt => 'S>' },
  :uint32 => { :size => 4, :fmt => 'L>' },
  :uint64 => { :size => 8, :fmt => 'Q>' }
}
FASTA_LINE_LEN = 
72

Class Method Summary collapse

Class Method Details

.handle_logging_options(opts) ⇒ Object 



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# File 'lib/bio/maf/parser.rb', line 1056

def handle_logging_options(opts)
  opts.on("--logger filename", String,
          "Log to file (default STDERR)") do |name|
    Bio::Log::CLI.logger(name)
  end
  opts.on("--trace options", String,
          "Set log level",
          "(default INFO, see bio-logger)") do |s|
    Bio::Log::CLI.trace(s)
  end
  opts.on("-q", "--quiet", "Run quietly") do
    Bio::Log::CLI.trace('error')
  end
  opts.on("-v", "--verbose", "Run verbosely") do
    Bio::Log::CLI.trace('info')
  end
  opts.on("--debug", "Run with extra debugging output") do
    Bio::Log::CLI.trace('debug')
  end
end