Table of Contents - bio-maf-1.0.1 Documentation
Pages
- LICENSE
-
README
- bio-maf
- Dependencies
- Installation
- Performance
- Usage
- Create an index on a MAF file
- Compress and index a MAF file
- Extract blocks from an indexed MAF file, by genomic interval
- Extract alignment blocks truncated to a given interval
- Filter species returned in alignment blocks
- Extract blocks matching certain conditions
- Match only blocks with all specified species
- Match only blocks with a certain number of sequences
- Match only blocks within a text size range
- Process each block in a MAF file
- Parse empty (āeā) lines
- Remove gaps from parsed blocks
- Join blocks after filtering together
- Extract bio-alignment representations of blocks
- Tile blocks together over an interval
- Compression
- Command line tools
- Other documentation
- Project home page
- Cite
- Biogems.info
- Copyright
Classes and Modules
- Bio
- Bio::GenomicInterval
- Bio::MAF
- Bio::MAF::Access
- Bio::MAF::AllSpeciesFilter
- Bio::MAF::AtLeastNSequencesFilter
- Bio::MAF::BGZFChunkReader
- Bio::MAF::Block
- Bio::MAF::ChunkReader
- Bio::MAF::CompletionTracker
- Bio::MAF::DummyExecutor
- Bio::MAF::DummyParser
- Bio::MAF::EmptySequence
- Bio::MAF::Executor
- Bio::MAF::FASTARangeReader
- Bio::MAF::FASTAWriter
- Bio::MAF::Filter
- Bio::MAF::Filters
- Bio::MAF::ForkRunner
- Bio::MAF::Header
- Bio::MAF::JExecutor
- Bio::MAF::JThreadRunner
- Bio::MAF::JobRunner
- Bio::MAF::KVHelpers
- Bio::MAF::KyotoIndex
- Bio::MAF::MAFParsing
- Bio::MAF::MaxSizeFilter
- Bio::MAF::Member
- Bio::MAF::MinSizeFilter
- Bio::MAF::ParseContext
- Bio::MAF::ParseError
- Bio::MAF::Parser
- Bio::MAF::Sequence
- Bio::MAF::Struct
- Bio::MAF::ThreadedChunkReaderWrapper
- Bio::MAF::Tiler
- Bio::MAF::Writer
- Bio::Ucsc
- Bio::Ucsc::UcscBin
- BioMaf
Methods
- ::bin — Bio::Ucsc::UcscBin
- ::bin_all — Bio::Ucsc::UcscBin
- ::bin_all_extended — Bio::Ucsc::UcscBin
- ::bin_all_standard — Bio::Ucsc::UcscBin
- ::bin_from_range — Bio::Ucsc::UcscBin
- ::bin_from_range_extended — Bio::Ucsc::UcscBin
- ::bin_from_range_standard — Bio::Ucsc::UcscBin
- ::build — Bio::MAF::KyotoIndex
- ::build — Bio::MAF::Filters
- ::create — Bio::MAF::JobRunner
- ::create — Bio::MAF::Executor
- ::default — Bio::MAF::Header
- ::file — Bio::MAF::Access
- ::handle_logging_options — Bio::MAF
- ::maf_dir — Bio::MAF::Access
- ::new — Bio::MAF::Access
- ::new — Bio::MAF::KyotoIndex
- ::new — Bio::MAF::AllSpeciesFilter
- ::new — Bio::MAF::AtLeastNSequencesFilter
- ::new — Bio::MAF::MaxSizeFilter
- ::new — Bio::MAF::MinSizeFilter
- ::new — Bio::MAF::Filters
- ::new — Bio::MAF::ForkRunner
- ::new — Bio::MAF::JThreadRunner
- ::new — Bio::MAF::JExecutor
- ::new — Bio::MAF::DummyExecutor
- ::new — Bio::MAF::Header
- ::new — Bio::MAF::Block
- ::new — Bio::MAF::Sequence
- ::new — Bio::MAF::EmptySequence
- ::new — Bio::MAF::ChunkReader
- ::new — Bio::MAF::BGZFChunkReader
- ::new — Bio::MAF::ThreadedChunkReaderWrapper
- ::new — Bio::MAF::ParseContext
- ::new — Bio::MAF::Parser
- ::new — Bio::MAF::CompletionTracker
- ::new — Bio::MAF::Struct
- ::new — Bio::MAF::Member
- ::new — Bio::MAF::Tiler
- ::new — Bio::MAF::FASTARangeReader
- ::new — Bio::MAF::Writer
- ::new — Bio::MAF::FASTAWriter
- ::open — Bio::MAF::KyotoIndex
- #<< — Bio::MAF::CompletionTracker
- #_merge_bgzf_fetch_list — Bio::MAF::Parser
- #_merge_fetch_list — Bio::MAF::Parser
- #_parse_block — Bio::MAF::MAFParsing
- #_parse_header — Bio::MAF::Parser
- #_slice — Bio::MAF::Block
- #_slice_text_range — Bio::MAF::Block
- #_wrap — Bio::MAF::Parser
- #add — Bio::MAF::ForkRunner
- #add — Bio::MAF::JThreadRunner
- #append_chunks_to — Bio::MAF::ParseContext
- #await — Bio::MAF::ForkRunner
- #bin — Bio::GenomicInterval
- #bin_all — Bio::GenomicInterval
- #bin_start_prefix — Bio::MAF::KVHelpers
- #block_joiner — Bio::MAF::Parser
- #build — Bio::MAF::KyotoIndex
- #build_bio_alignment — Bio::MAF::Tiler
- #build_block_value — Bio::MAF::KyotoIndex
- #call — Bio::MAF::Filter
- #can_start? — Bio::MAF::ForkRunner
- #check_chunk_size — Bio::MAF::ChunkReader
- #check_for_errors — Bio::MAF::JExecutor
- #chrom_index — Bio::MAF::Access
- #chunk_size= — Bio::MAF::ChunkReader
- #close — Bio::MAF::Access
- #close — Bio::MAF::KyotoIndex
- #close — Bio::MAF::Parser
- #close — Bio::MAF::FASTAWriter
- #context — Bio::MAF::Parser
- #conv_map — Bio::MAF::Parser
- #conv_send — Bio::MAF::Parser
- #decode_status_char — Bio::MAF::Sequence
- #delete_text — Bio::MAF::Sequence
- #drain_delayed — Bio::MAF::CompletionTracker
- #dump — Bio::MAF::KyotoIndex
- #each_block — Bio::MAF::Parser
- #each_block_seq — Bio::MAF::Parser
- #each_raw_seq — Bio::MAF::Block
- #empty? — Bio::MAF::Filters
- #empty? — Bio::MAF::Sequence
- #empty? — Bio::MAF::EmptySequence
- #end — Bio::MAF::Sequence
- #entries_for — Bio::MAF::KyotoIndex
- #extract_index_offset — Bio::MAF::KVHelpers
- #extract_n_sequences — Bio::MAF::KVHelpers
- #extract_species_vec — Bio::MAF::KVHelpers
- #extract_text_size — Bio::MAF::KVHelpers
- #extractor_fmt — Bio::MAF::Struct
- #f — Bio::MAF::ThreadedChunkReaderWrapper
- #fasta_desc — Bio::MAF::Sequence
- #fetch_blocks — Bio::MAF::ParseContext
- #fetch_blocks — Bio::MAF::Parser
- #fetch_blocks_merged — Bio::MAF::Parser
- #fetch_blocks_merged_parallel — Bio::MAF::Parser
- #fetch_list — Bio::MAF::KyotoIndex
- #fill_char= — Bio::MAF::Tiler
- #filter_seq_count — Bio::MAF::Parser
- #filtered? — Bio::MAF::Block
- #find — Bio::MAF::Access
- #find — Bio::MAF::KyotoIndex
- #find_gaps — Bio::MAF::Block
- #find_index_file — Bio::MAF::Access
- #flatten_vars — Bio::MAF::Writer
- #fmt — Bio::MAF::Struct
- #gapped? — Bio::MAF::Sequence
- #gather_leading_fragment — Bio::MAF::MAFParsing
- #handle_logging_options — Bio::MAF
- #index_blocks — Bio::MAF::KyotoIndex
- #intersection — Bio::GenomicInterval
- #interval — Bio::MAF::Sequence
- #join — Bio::MAF::Block
- #join — Bio::MAF::Sequence
- #join — Bio::MAF::EmptySequence
- #joinable_with? — Bio::MAF::Block
- #joinable_with? — Bio::MAF::Sequence
- #left_count — Bio::MAF::Sequence
- #left_status — Bio::MAF::Sequence
- #left_status_char — Bio::MAF::Sequence
- #load_index_sequences — Bio::MAF::KyotoIndex
- #load_species — Bio::MAF::KyotoIndex
- #make_scan_worker — Bio::MAF::KyotoIndex
- #make_worker — Bio::MAF::Parser
- #match — Bio::MAF::AllSpeciesFilter
- #match — Bio::MAF::AtLeastNSequencesFilter
- #match — Bio::MAF::MaxSizeFilter
- #match — Bio::MAF::MinSizeFilter
- #match — Bio::MAF::Filters
- #merge_fetch_list — Bio::MAF::Parser
- #next_expected — Bio::MAF::CompletionTracker
- #non_fill_re — Bio::MAF::Tiler
- #output_text — Bio::MAF::Tiler
- #overlaps? — Bio::MAF::KyotoIndex
- #parse_block — Bio::MAF::Parser
- #parse_block_data — Bio::MAF::MAFParsing
- #parse_blocks — Bio::MAF::Parser
- #parse_blocks_parallel — Bio::MAF::Parser
- #parse_empty — Bio::MAF::ParseContext
- #parse_empty_line — Bio::MAF::MAFParsing
- #parse_error — Bio::MAF::MAFParsing
- #parse_extended — Bio::MAF::ParseContext
- #parse_maf_vars — Bio::MAF::MAFParsing
- #parse_seq_line — Bio::MAF::MAFParsing
- #parse_trailing_fragment — Bio::MAF::MAFParsing
- #pos — Bio::MAF::BGZFChunkReader
- #position_at_start — Bio::MAF::FASTARangeReader
- #prep — Bio::MAF::KyotoIndex
- #raw_seq — Bio::MAF::Block
- #read_ahead — Bio::MAF::ThreadedChunkReaderWrapper
- #read_chunk — Bio::MAF::ChunkReader
- #read_chunk — Bio::MAF::BGZFChunkReader
- #read_chunk — Bio::MAF::ThreadedChunkReaderWrapper
- #read_chunk_at — Bio::MAF::ChunkReader
- #read_chunk_at — Bio::MAF::BGZFChunkReader
- #read_chunk_at — Bio::MAF::ThreadedChunkReaderWrapper
- #read_interval — Bio::MAF::FASTARangeReader
- #ref_data — Bio::MAF::Tiler
- #ref_seq — Bio::MAF::Block
- #reference= — Bio::MAF::Tiler
- #register_index — Bio::MAF::Access
- #remove_gaps! — Bio::MAF::Block
- #reopen — Bio::MAF::KyotoIndex
- #right_count — Bio::MAF::Sequence
- #right_status — Bio::MAF::Sequence
- #right_status_char — Bio::MAF::Sequence
- #run — Bio::MAF::ForkRunner
- #run — Bio::MAF::JThreadRunner
- #runs — Bio::MAF::Tiler
- #scan_bin — Bio::MAF::KyotoIndex
- #scan_bins — Bio::MAF::KyotoIndex
- #scan_bins_parallel — Bio::MAF::KyotoIndex
- #scan_dir — Bio::MAF::Access
- #scoring — Bio::MAF::Header
- #seq_filter_ok? — Bio::MAF::MAFParsing
- #seq_from — Bio::MAF::Block
- #seq_id_for — Bio::MAF::KyotoIndex
- #sequence_filter — Bio::MAF::ParseContext
- #sequence_filter — Bio::MAF::Parser
- #sequence_filter= — Bio::MAF::Parser
- #set_last_block_pos! — Bio::MAF::ParseContext
- #set_last_block_pos! — Bio::MAF::MAFParsing
- #shutdown — Bio::MAF::JExecutor
- #shutdown — Bio::MAF::DummyExecutor
- #slice — Bio::MAF::Access
- #slice — Bio::MAF::KyotoIndex
- #slice — Bio::MAF::Block
- #slice — Bio::MAF::Sequence
- #slice — Bio::MAF::EmptySequence
- #species — Bio::MAF::Sequence
- #species_for_output — Bio::MAF::Tiler
- #species_id_for_seq — Bio::MAF::KyotoIndex
- #species_to_use — Bio::MAF::Tiler
- #start_chunk_read_if_needed — Bio::MAF::ParseContext
- #start_job — Bio::MAF::ForkRunner
- #start_read_ahead — Bio::MAF::ThreadedChunkReaderWrapper
- #submit — Bio::MAF::JExecutor
- #submit — Bio::MAF::DummyExecutor
- #text — Bio::MAF::EmptySequence
- #text_range — Bio::MAF::Sequence
- #text_size — Bio::MAF::Block
- #tile — Bio::MAF::Access
- #tile — Bio::MAF::Tiler
- #to_bio_alignment — Bio::MAF::Block
- #to_bio_alignment — Bio::MAF::Sequence
- #to_s — Bio::MAF::KyotoIndex
- #to_s — Bio::MAF::Block
- #trailing_nl? — Bio::MAF::MAFParsing
- #unpack_key — Bio::MAF::KVHelpers
- #upcase! — Bio::MAF::Block
- #upcase! — Bio::MAF::Sequence
- #upcase! — Bio::MAF::EmptySequence
- #version — Bio::MAF::Header
- #with_context — Bio::MAF::Parser
- #with_index — Bio::MAF::Access
- #with_parser — Bio::MAF::Access
- #with_profiling — Bio::MAF::KyotoIndex
- #wrap_block_seq — Bio::MAF::Parser
- #write_block — Bio::MAF::Writer
- #write_block — Bio::MAF::FASTAWriter
- #write_blocks — Bio::MAF::Writer
- #write_fasta — Bio::MAF::EmptySequence
- #write_fasta — Bio::MAF::Tiler
- #write_header — Bio::MAF::Writer
- #write_seq — Bio::MAF::Writer
- #write_sequence — Bio::MAF::FASTAWriter