Add reference sequence index cache to speed up query by 20% for certain
usecases
Merge pull request #23 from samtools/bw_skipToSequenceOptimization

Add reference sequence index cache to speed up query by 20% for certain
IntervalTreeMap added two method to test interval overlapping
Merge pull request #24 from samtools/pl_intervaltreemap

IntervalTreeMap added two method to test interval overlapping
Fix nullpointer exception when BAMFileSpan is null
Merge pull request #25 from samtools/bw_FileSpanBugfix

Fix nullpointer exception when BAMFileSpan is null
Dont iterate over bins that are not actually interesting
Merge pull request #26 from samtools/bw_BinningIndexContextSpeedup

Dont iterate over bins that are not actually interesting
Case of symbolic allele ID string now being preserved as per VCFv4.1 section 1.4.5
Merge pull request #27 from samtools/dc_sv_parsing_fix

Case of symbolic allele ID string now being preserved as per VCFv4.1 sec...
Detect old style metric file and skip over header reading code.
Merge pull request #29 from samtools/aw_handle_old_style_metrics

Detect old style metric file and skip over header reading code.
An easier way to handle old-style metrics files
Merge pull request #33 from samtools/jr_read_old_metrics

An easier way to handle old-style metrics files