CRAM queryUnmapped returns incorrect values with recordPerSlice=2000

[cmnbroad]

I used a large BAM file, converted to CRAM and compared the number of records returned from unmappedQuery:

BAM: 50,000 records
CRAM converted using samtools defaults: 50,000 records
CRAM converted using htsjdk: 50,000 records
CRAM converted using samtools, seqs_per_slice=2000: 65501 records

The file I used is too big to add as a test case, so we'll need to dig deeper to find out if the problem originates in the cram file, index generation, crai->bai conversion, or htsjdk query implementation.

[cmnbroad]

Closed via #552.