Handle thread output incrementally

[bkille]

• Moved the position-lookup construction code to the thread output handler, so that the map is incrementally constructed as each thread finishes processing a contig as opposed to doing it only once all contigs are indexed. Leads to a much more parallel index construction. Output remains unchanged.
• Improved the index-saving feature so that the frequent seeds are also saved.
• Slightly changed the logging text to be more precise.