factory bam writer
fixed format, added a test in SAMFileWriterFactoryTest
Slight refactor.
Merge pull request #13 from samtools/pl_sam_writer_factory_stream

Pl sam writer factory stream
40% speed improvement for query under certain workloads
Merge pull request #14 from samtools/bw_queryArrayListOptimization

40% speed improvement for query under certain workloads
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