Perform basic sanity checks upon loading an existing index (PRIVATE).

Indexes or loads the index of a MAF file.

Return the number of records in the index.

Return index information for each bundle (PRIVATE).

Yields index information for each bundle in the form of (bin, start, end, offset) tuples where start and end are 0-based inclusive coordinates.

Read MAF file and generate SQLite index (PRIVATE).

Retrieve a single MAF record located at the offset provided (PRIVATE).

Find bins that a region may belong to (PRIVATE).

Converts a region to a list of bins that it may belong to, including largest and smallest bins.

Return the smallest bin a given region will fit into (PRIVATE).

Adapted from http://genomewiki.ucsc.edu/index.php/Bin_indexing_system

Return a multiple alignment of the exact sequence range provided.

Accepts two lists of start and end positions on target_seqname, representing exons to be spliced in silico. Returns a MultipleSeqAlignment of the desired sequences spliced together.

starts should be a list of 0-based start coordinates of segments in the reference. ends should be the list of the corresponding segment ends (in the half-open UCSC convention: http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/).

To ask for the alignment portion corresponding to the first 100 nucleotides of the reference sequence, you would use search([0], [100])

Search index database for MAF records overlapping ranges provided.

Returns MultipleSeqAlignment results in order by start, then end, then internal offset field.

starts should be a list of 0-based start coordinates of segments in the reference. ends should be the list of the corresponding segment ends (in the half-open UCSC convention: http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/).