Suppose you have a region [beg, end) and want to do a query.
Here's the reference: [....................!..............!.................................] beg end
Here's the same reference with 16384-byte long windows: [%...........%.......!....%.........!..%...........%...........%......] beg end [ 1st window][ 2nd window][...
With linear index, we can take the second window, find out what is the minimum virtual offset among alignments overlapping this window, and skip all chunks which end position is less or equal to this offset:
[........@...........!..............!.................................] . ..min. offset beg end [ ). . <- this chunk is skipped [ ) <- this one is not
Virtual file offsets of first alignments overlapping 16384-byte windows on the reference sequence. This linear index is used to reduce amount of file seeks for region queries, since with its help one can reduce the number of chunks to be investigated based on their end position.