adding a tool to convert BED files to Picard Interval Lists.
Merge pull request #50 from broadinstitute/nh_bed_to_interval_list

adding a tool to convert BED files to Picard Interval Lists.
adding the ability to add the full five fields when creating an interval
list from a BED
adding the strand and name when converting BED to interval_list
Merge pull request #55 from broadinstitute/nh_bed_to_interval_list

adding the ability to add the full five fields when creating an interval
BUGFIX: BedToIntervalList would not accept an input BED interval was one base long

Added a few more tests for other valid and invalid cases
small improvement to the warning message
fixing some small javadoc warnings in picard
Make the release script push releases, javadoc, and the website
documentation to github pages rather than sourceforge.

Removed the static pages in src/www that are put on the gh-pages branch

README.md points to the Picard documentation github pages site

Due to html5, we shoul change <a name=""/> to be <a id=""/>.
Release 1.120
Fix issue with VALIDATION_STRINGENCY not being propagated.
Merge pull request #60 from broadinstitute/kt_revert_sam_propagate_validation_stringency

Fix issue with VALIDATION_STRINGENCY not being propagated.
release script fixed to work with releasing to github: the javadoc
directory was incorrect
Merge pull request #61 from broadinstitute/nh_working_github_release_script

release script fixed to work with releasing to github: the javadoc
Modify SANITIZE method of ReverSam to convert all non-Standard quality score encoding schemes to Standard.
Bugfix: the validation stringency command line option is now passed to
the sam reader factory
Merge pull request #63 from broadinstitute/kt_revert_sam_all_quality_scores_standard

Modify SANITIZE method of ReverSam to convert all non-Standard quality s...
Merge pull request #62 from broadinstitute/nh_bugfix_validation_stringency_on_sam_reader_factory

Bugfix: the validation stringency command line option is now passed to
Removed redundant IOUtil.openFileForWriting() calls for the fastq writers.
Moved the test for duplicate @PD.IDs into AbstractAlignmentMerger to avoid opening the unmapped SAM file twice.