bend-edit-distance

Releases (4)

• 0.2.2.0 indexed
• 0.2.1.0 unindexed
• 0.2.0.0 unindexed
• 0.1.0.0 unindexed

Definitions (210)

src/Myers.bend

• type Block
• type CarryHorizontal differences are -1, 0, or +1.
• def split_query.prepend
• def split_query
• def build_peq_wordBit i matches query[i] literally or through an explicit symmetric pair.
• def build_peq_tableA byte-indexed immutable table replaces the C++ transformed alphabet.
• def peq_get
• def build_peq.step
• def build_peq
• def ceil_div
• def init_blocks
• def calculate_blockcalculateBlock / Advance_Block from Myers.
• def advance_column.stepA column and consecutive target columns depend on their predecessor; parallelizing those calls would violate the Myers carry dependency.
• def advance_column
• def get_block_cell_valuegetBlockCellValues(block)[W], without constructing the other 31 cells.
• def last_block_score
• type BandEntryAn active entry owns its current block and shares its immutable profile.
• type Band
• type UpdatedBand
• type BandStep
• type SearchWork counts actual calculate_block calls, consumed columns and fresh attempts.
• def init_band_entries.step
• def init_band_entries
• def init_band.step
• def init_band
• def advance_band.join
• def advance_band.last
• def advance_band.next
• def advance_band
• def band_keep_lastEdlib's conservative Ukkonen block bounds, rearranged so every term is nonnegative Nat arithmetic.
• def band_keep_first
• def trim_last.choose
• def trim_last.join
• def trim_last
• def trim_first.step
• def trim_first
• def reduce_band.step
• def reduce_band
• def expand_band.step
• def expand_band
• def band_step.updated
• def band_step
• def band_last_score
• def band_finish
• def myers_calc_edit_distance_nw.step
• def myers_calc_edit_distance_nw
• def band_attempt
• def adaptive_search.step
• def adaptive_search.result
• def adaptive_search
• def search_profiles
• def search_query
• def search_shorter
• def semiglobal_carryDirectional modes never swap query and target.
• def init_semiglobal_band
• def trim_semiglobalIf the bottom score is >= k+32 every cell in that block is > k.
• def reduce_semiglobal
• def expand_semiglobal.result
• def expand_semiglobal.choose
• def expand_semiglobal
• def semiglobal_step
• def semiglobal_endpoint
• def myers_calc_edit_distance_semiglobal.step
• def myers_calc_edit_distance_semiglobalDecode the real last query cell at every column, without Edlib's delayed padded endpoints.
• def semiglobal_initial_best
• def semiglobal_maximum
• def semiglobal_best
• def hw_startEdlib selects the LAST optimal reverse-SHW end, hence the earliest start for each forward end.
• def hw_start_best
• def hw_location
• def hw_locationsIndependent starts share one reversed query profile.
• def configured_found
• def configured_result
• def configured_finish
• def semiglobal_align
• def search_distance
• def found_value
• def align_shorter
• def distance
• def nw_result
• def edlib_align
• def response

src/Reconstruction.bend

• def diagonal_operation
• type TraceCell
• def cell_score
• def choose_operation
• def dp_cell
• def dp_row_cells
• def dp_row
• def dp_initial
• def dp_rows
• def tracebackRows and their operations are reversed so left moves consume the current row directly.
• def dp_trace
• def dp
• def small_matrixBound the complete small matrix, including its boundary cells.
• def score_row
• type Split
• def split_index
• def split_score
• def split_update