Robert Buels

NAME

Bio::JBrowse::Store::NCList - stores feature data in an on-disk lazy nested-containment list optimized for fetching over HTTP

SYNOPSIS

  my $store = Bio::JBrowse::Store::NCList->new({
      path   => "path/to/directory"
  });

  # insert plain hashrefs of feature data into the store
  $store->insert( $stream, ... );
  $store->insert_presorted( $sorted_stream, ... );

METHODS

new( \%args )

 Create a new store, overwriting any existing files.

Arguments

path

path to the directory in which to put the formatted files

compress

if true, store the data files in gzipped format

insert_presorted( $stream, ... )

Insert the feature hashrefs from the given pre-sorted stream(s) into the NCList store. Streams must be sorted by reference sequence name ascending, then start coordinate ascending.

A stream is just a subroutine ref that returns a series of single hashrefs when called repeatedly, then returns nothing when the stream is at an end.

insert( $stream, ... )

Insert the feature hashrefs from the given unsorted stream(s) into the NCList store.

Sorts the contents of the streams using Sort::External before loading it into the NCList store.

A stream is just a subroutine ref that returns a series of single hashrefs when called repeatedly, then returns nothing when the stream is at an end.

AUTHOR

Robert Buels <rbuels@gmail.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by Robert Buels.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.