type item = {matches : int;number of bases that match that aren't repeats
*)mismatches : int;number of bases that don't match
*)rep_matches : int;number of bases that match but are part of repeats
*)n_count : int;number of 'N' bases
*)q_num_insert : int;number of inserts in query
*)q_base_insert : int;number of bases inserted in query
*)t_num_insert : int;number of inserts in target
*)t_base_insert : int;number of bases inserted in target
*)q_name : string;query sequence name
*)q_strand : char;'+' or '-' for query strand
*)q_size : int;query sequence size
*)q_start : int;alignment start position in query
*)q_end : int;alignment end position in query
*)t_name : string;target sequence name
*)t_strand : char option;target strand for translated alignments
*)t_size : int;target sequence size
*)t_start : int;alignment start position in target
*)t_end : int;alignment end position in target
*)block_count : int;number of blocks in the alignment (a block contains no gaps)
*)block_sizes : int list;sizes of each block
*)q_starts : int list;starting positions of each block in query
*)t_starts : int list;starting positions of each block in target
*)}PSL files. Tested only on PSL files generated by BLAT version 34, which output psLayout version 3 files.
module Error : sig ... endexception Error of Error.tval in_channel_to_item_stream :
?buffer_size:int ->
?filename:string ->
Core_kernel.In_channel.t ->
(item, [> Error.t ]) Core_kernel.result Stdlib.Stream.tval in_channel_to_item_stream_exn :
?buffer_size:int ->
?filename:string ->
Core_kernel.In_channel.t ->
item Stdlib.Stream.tmodule Transform : sig ... endval line_to_item : Pos.t -> Line.t -> (item, Error.t) Core_kernel.resultval item_of_sexp : Sexplib.Sexp.t -> itemval sexp_of_item : item -> Sexplib.Sexp.t