Merged bug fix from Stable into Unstable
Merged bug fix from Stable into Unstable
Update expected test output for Java 7

-Changes in Java 7 related to comparators / sorting produce a large number
 of innocuous differences in our test output. Updating expectations now
 that we've moved to using Java 7 internally.

-Also incorporate Eric's fix to the GATKSAMRecordUnitTest to prevent
 intermittent failures.
Merge pull request #206 from broadinstitute/dr_update_tests_for_java7

Update expected test output for Java 7
Adding argument to CGL to not stratify by sample name. This is useful when running with 1000G so that you don't get 1000s of lines on the plots.
Merge pull request #204 from broadinstitute/rp_cgl_force_sample_name

Adding argument to CGL to not stratify by sample name. This is useful wh...
- Fixed a small bug in the printout of molten data in GenotypeConcordance
Output didn't "mix-up" the genotypes, it outputed the same HET vs HET (e.g.) 3 times rather than the combinations of HET vs {HET, HOM, HOM_REF}, etc.
This was only a problem in the text, _not_ the actual numbers, which were outputted correctly.

- Updated MD5's after looking at diffs to verify that the change is what I expected.
Fixing the bundle script

1. someone out there busted it when adding high confidence 1000G calls
2. new path to NA12878 bam
3. updated clashing version argument
Adding .fai file to example fasta since we don't generate it anymore
Merge pull request #207 from broadinstitute/eb_fixing_bundle_script

Fixing the bundle script
Revert changes to exampleFASTA.fasta.fai for now to get tests passing again
Now that we don't generate dict and fai files, the resource script needs to copy them to the bundle.
Merge pull request #209 from broadinstitute/eb_more_fixes_to_bundle_script

Now that we don't generate dict and fai files, the resource script needs...
Rev'd up Picard to get PL fix: PLs were saturated to 32767 (Short.MAX_VALUE) when converting from GL to integers. Increase capping to Integer.MAX_VALUE (2^31-1) which should be enough for reasonable sites now. Integration tests change because some tests have some hyper-deep pileups where this case was hit
Starting NA12878 KB requires use Java-1.7
Merge pull request #211 from broadinstitute/md_kb_script

Starting NA12878 KB requires use Java-1.7
Merge pull request #210 from broadinstitute/gda_QUAL_fix_GSA-910

Rev'd up Picard to get PL fix: PLs were saturated to 32767 (Short.MAX_VA...
leftAlignCigarSequentially now supports haplotypes with insertions and deletions where the deletion allele was previously removed by the leftAlignSingleIndel during it's cleanup phase.
Bugfix for AlignmentUtils.trimCigarByBases

-- Previous version would trim down 2M2D2M into 2M if you asked for the first 2 bases, but this can result in incorrect alignment of the bases to the reference as the bases no longer span the full reference interval expected.  Fixed and added unit tests
Utils.dupString should allow 0 number of duplicates to produce empty string