Fixup imports and class references that are a consequence of htsjdk's `SamReaderFactory` refactor.
Merge pull request #4 from broadinstitute/mm_import_fixup

Fixup imports and class references that are a consequence of htsjdk's `SamReaderFactory` refactor.
Unit test for GatherBamFiles
Merge pull request #5 from broadinstitute/jg_pfb409

Unit test for GatherBamFiles
Add new modes to `IntervalListTools`.
- `INTERVAL_SUBDIVISION`, which is the default mode, and functions like the previous version of `IntervalListTools`.
- `BALANCING_WITHOUT_INTERVAL_SUBDIVISION`, which emits interval lists without splitting them up, and sizes the output interval list sizes to be no smaller than the largest input interval.
- Bug fix: don't emit empty intervals.
IntelliJ auto change
Release 1.114
Get javadoc building.
Get tagging working with github
Merge pull request #6 from broadinstitute/mm_interval_list_tools_atomic_scattering

Add new modes to `IntervalListTools`.
Enable `CollectTargetedPcrMetrics` and `CalculateHsMetrics` to target multiple baitsets.
- Both command line programs' `TARGET_INTERVALS` argument accept multiple values.
- `CalculateHsMetrics`'s `BAIT_INTERVALS` accepts multiple values.
Merge pull request #7 from broadinstitute/mm_targeted_metrics_multiple_interval_lists

Enable `CollectTargetedPcrMetrics` and `CalculateHsMetrics` to target multiple baitsets.
Get working with git
bug fix -- missing popd
Include htsjdk jar in deployment zip.
Merge pull request #10 from broadinstitute/aw_fix_release_script

Aw fix release script
Remove dependence on JAVA6_HOME environment variable.
Merge pull request #11 from broadinstitute/aw_remove-java6-home

Remove dependence on JAVA6_HOME environment variable.
Update release_picard.sh

Run both picard and htsjdk unit test suites.
Indicate in INPUT doc string that may not be streamed.