Added CustomReaderFactory for plugging in external implementations of SamReader capable of getting data from APIs.
Fixed a bug in VCFUtils.smartMergeHeaders

When merging VCFHeaders, this method was scrambling the order of the VCFHeaderLines

This ordering is depended upon elsewhere, such as the VCFHeader.getSequenceDictionary method.
As a result, merged headers would present scrambled sequence dictionaries.

Fixed this method to return VCFHeaderLines in order.
A little cleanup and conversion of SamLocusIterator to use ArrayLists instead of LinkedLists for about 30% speedup.
More performance optimizations of accumulateSamRecord()
More cleanup and documentation.
Merge pull request #107 from samtools/bt_VCF_header_merging_bugfix

Fixed a bug in VCFUtils.smartMergeHeaders
only return the first error when validating a SAMRecord using STRICT
Merge pull request #109 from samtools/nh_faster_samrecord_validation_failure

only return the first error when validating a SAMRecord using STRICT
running 'execstack -c' on the libIntelDeflater.so to resolve a JVM warning
Merge pull request #112 from samtools/nh_execstack_fix

running 'execstack -c' on the libIntelDeflater.so to resolve a JVM warni...
Merge pull request #98 from iliat/ga4gh-work

First step in adding support for getting Reads data from APIs such as Google Genomics
removing unused import in the CustomReaderFactory
Merge pull request #114 from samtools/nh_remove_unused_import

removing unused import in the CustomReaderFactory
Fixed bug in setSequenceDictionary where assembly value not being set properly in VCF header
Results of code review - comment, fixing indent
Initial maven-ization.  Also added example keystore to use for signing jars.
Replaced use of TestNG in SAMTestUtil.
Generate sources and javadoc jars
Remove ranged versioned dependencies
Remove bcel and ant from maven dependencies
Clean up spacing; maven requests 2-space indents for POMs.
Add release profile, and move to maven-gpg-plugin instead of maven-jarsigner-plugin.
Adding oss-sonatype parent, XML version, and adding Nils Homer as Broad PoC for HTSJDK.
Adding dependency management section.
Added reasonable version ranges to mitigate potential version conflicts. When the build fails due to minor, generally backwards-compatible version increments, the better solution would be to figure out why it fails and to fix it (e.g. for snappy-java). Feel free to tighten or expand these ranges.
In build.xml, changed htsjdk.version.property.xml to htsjdk.version.properties. See https://github.com/samtools/htsjdk/issues/99
Changed .gitignore and build.xml according to https://github.com/samtools/htsjdk/pull/113