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.
Synchronize on the 'out' PrintStream instead of 'this' to avoid mixing
up log statements from different threads. Example from actual log file:

DEBUG	DEBUG	2014-06-02 08:48:46	IlluminaBasecallsConverter	Reading data
from tile 11206 ...
2014-06-02 08:48:46	IlluminaDataProviderFactory	The following parsers
will be used by IlluminaDataProvider:
An easier way to handle old-style metrics files
Add additional boolean genotype functions to JEXLMap to add functionality to GATK tools using JEXL (like VariantFiltration)
Merge pull request #33 from samtools/jr_read_old_metrics

An easier way to handle old-style metrics files
Merge pull request #32 from samtools/ldg_newJEXLmapGTs

Add additional boolean genotype functions to JEXLMap to add functionalit...
Bug fix in `RelativeIso8601Date`: non-lazy times are not deserialized properly.
FastqRecord: added methods equals, hashcode, toString, length
Merge pull request #37 from lindenb/fastq2

FastqRecord: added methods equals, hashcode, toString, length