Clean up cruft
removed properties and classpath which are no longer used
Merge pull request #16 from samtools/bp_build_clean

removed properties and classpath which are no longer used
Better message when reference fasta index does not exist.
Updated eclipse references
Added java test cases to src
Accepting VCF 4.2 breakend and inline symbolic insertion alleles
VariantContextBuilder: no longer crashing when an attribute is set without loading attributes or explicitly calling .attributes(null) first
Better comment.
Merge pull request #17 from samtools/dc_vcb_bug_fix_and_symb_allele

Dc vcb bug fix and symb allele
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...