Merge all FilePointers for each contig into a single, merged, optimized FilePointer
representing all regions to visit in all BAM files for a given contig.
This helps us in several ways:
-It allows us to create a single, persistent set of iterators for each contig,
finally and definitively eliminating all Shard/FilePointer boundary issues for
the new experimental ReadWalker downsampling
-We no longer need to track low-level file positions in the sharding system (which
was no longer possible anyway given the new experimental downsampling system)
-We no longer revisit BAM file chunks that we've visited in the past -- all BAM
file access is purely sequential
-We no longer need to constantly recreate our full chain of read iterators
There are also potential dangers:
-We hold more BAM index data in memory at once. Given that we merge and optimize
the index data during the merge, and only hold one contig's worth of data at a
time, this does not appear to be a major issue. TODO: confirm this!
-With a huge number of samples and intervals, the FilePointer merge operation
might become expensive. With the latest implementation, this does not
appear to be an issue even with a huge number of intervals (for one sample, at least),
but if it turns out to be a problem for > 1 sample there are things we can do.
Still TODO: unit tests for the new FilePointer.union() method
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