Added an option to VCFWriter to write the entire FORMAT field, even if the trailing values are missing and could therefore be trimmed.  Also fixed ParsingUtils.split() to correctly handle the case where the only delimiter is the first character
Merge pull request #96 from pdexheimer/pd_trailing_format_fields

Added an option to VCFWriter to write the entire FORMAT field, even if t...
Release 1.120
README.md points to the HTSJDK documentation github pages site
The SamReaderFactory needs to expose a way to set the default validation
stringency
Merge pull request #100 from samtools/nh_readme_doc_update

README.md points to the HTSJDK documentation github pages site
Merge pull request #101 from samtools/nh_bugfix_validation_stringency_on_sam_reader_factory

The SamReaderFactory needs to expose a way to set the default validation
do not enforce by default that intervals that will be merged have the
same strand
Merge pull request #102 from samtools/nh_interval_merging_ignores_strands

do not enforce by default that intervals that will be merged have the
Adding copyrights to some recently added classes
added methods to check for readability/writability of list of files
Merge pull request #105 from samtools/nh_add_copyright

Adding copyrights to some recently added classes
Merge pull request #106 from samtools/nh_add_to_ioutil

added methods to check for readability/writability of list of files
adding methods to help set mate cigars and mate information given a
queryname sorted iterator.  This is useful when we want to fix or update
the mate information, including the mate cigar.
Merge pull request #103 from samtools/nh_really_fix_supplementals

adding a method to help set mate cigars and mate information given a
Fixes related to JDK8 in SamFileHeaderMergerTest

1. SAM test files had spaces as delimiters in
   some headers (spec requires tab delimiters)
2. The order of attributes in merged headers
   is non-deterministic (and turns out to be
   different in jdk8 than in earlier versions).
   This tests the headers independent of
   attribute order.
3. jdk8 tearDown complains when tmpDir is empty
   in SortingCollectionTest, earlier jdks
   ignored this.
travis tests on oraclejdk8
Merge pull request #89 from bpow/SAMFileHeaderMergerTest-order

SAMFileMergerTest relies on HashMap ordering produced by jdk6/7
Add the option of using original quality scores for determining the encoding scheme.
Merge pull request #104 from samtools/kt_revert_sam_use_oq_for_detection

Add the option of using original quality scores for determining the enco...