Bug fix: `IndexStreamBuffer` prematurely throws data-exhaustion error.
- When fewer than the requested number of bytes are read from a stream, keep reading until the stream is actually exhausted.
Merge pull request #75 from samtools/mm_bugfix_bam_index_input_stream_api_compliance

Bug fix: `IndexStreamBuffer` prematurely throws data-exhaustion error.
Bug fix: if `this` has a field with value `null`, `equals()` throws a `NullPointerException` despite that being a valid state.
Merge pull request #77 from samtools/mm_bugfix_metrics_equals

MetricBase NPE fix
Release 1.119
Removed closing of internal output stream directly in the BCF2Writer.

BCF2Writer.close() was calling outputStream.close() and then super.close();
but in IndexingVariantContextWriter's (the super class of BCF2Writer) close() method
it also calls outputStream.close().  So we were double-closing the output stream.

This manifests itself as a problem when we try to write e.g. a compressed bcf file
because the close method tries to do a final write (which fails on the 2nd close).
Ignore symbolic alleles when running strict validation for a VCF.

We often expect symbolic alleles not to show up in the genotypes (e.g. with NON_REF alleles).
Merge pull request #80 from eitanbanks/eb_fix_gvcf_validation

Ignore symbolic alleles when running strict validation for a VCF.
Merge pull request #79 from eitanbanks/master

Removed closing of internal output stream directly in the BCF2Writer.
Added additional methods to support detection from an iterator of SAMRecords.
Added wrapping of FileOutputStreams with BufferedOutputStreams in FileAppendStreamLRUCache.
Merge pull request #82 from samtools/tf_file_stream_lru_cache_fix

Added wrapping of FileOutputStreams with BufferedOutputStreams in FileAp...
Added additional methods to support detection from an iterator of SAMRecords.
Changes per code review.
Merge branch 'kt_fix_quality_score_encoding' of github.com:samtools/htsjdk into kt_fix_quality_score_encoding

Conflicts:
	src/java/htsjdk/samtools/util/QualityEncodingDetector.java
Failed to resolve all conflicts in the prior merge.
Merge pull request #81 from samtools/kt_fix_quality_score_encoding

Added additional methods to support detection from an iterator of SAMRecords to SANITIZE
add ability to set the mate cigar on supplementary alignments
Merge pull request #83 from samtools/nh_bwa_mem_output_suppl

add ability to set the mate cigar on supplementary alignments
Initial commit supporting MarkDuplicatesWithMateCigar

These changes were from before the Picard-public/htsjdk split. This branch is synchronous with the branch of the same name in Picard-public