Module: Bio::MAF
- Defined in:
- lib/bio/maf/parser.rb,
lib/bio/maf/maf.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: KVHelpers, MAFParsing Classes: Access, AllSpeciesFilter, AtLeastNSequencesFilter, Block, ChunkReader, CompletionTracker, DummyParser, EmptySequence, FASTARangeReader, FASTAWriter, Filter, Filters, Header, KyotoIndex, MaxSizeFilter, Member, MinSizeFilter, ParseContext, ParseError, Parser, Sequence, Struct, ThreadedChunkReader, 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 905 def (opts) opts.on("--logger filename", String, "Log to file (default STDOUT)") 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 |