consider soft clipping at the ends of reads when clipping reads that
overhang the reference
Merge pull request #97 from broadinstitute/nh_off_the_end_clip_fix

consider soft clipping at the ends of reads when clipping reads that
Added a button  to the explain-flags.html page. This button switches the flag from the flag of a read, to that of its mate (as much as can be infered).
Merge pull request #94 from broadinstitute/yf_add_switch_to_mate_for_explain_sam_flags

Added a button to the explain-flags.html page
make getProgramProperty public for things that need to check annotations
Merge pull request #98 from broadinstitute/nh_make_clp_function_pub

make getProgramProperty public for things that need to check annotations
adding in a command line tool to rename a sample in a vcf
Merge pull request #99 from broadinstitute/nh_add_rename_sample_in_vcf

adding in a command line tool to rename a sample in a vcf
Moved from private to public.

responded to reviewer comments.

added tests.
Merge pull request #100 from broadinstitute/yf_IlluminaFilters

New CLP to collect coverage information according to Illumina-defined filters.
I screwed up with the directories when I moved this from private to public.

This commit fixes the problem.
Merge pull request #102 from broadinstitute/yf_fix_illumina_metric_directory

I screwed up with the directories when I moved this from private to public
Addressed PR comments, squashed and rebased.
Fix compile error
Merge pull request #101 from broadinstitute/mds_expand_gc_metrics

Added CONTINGENCY_VALUES column to detailed metrics. Added new GenotypeC...
picard version 1.124

picard version 1.124
Add new statistic 'Specificity' to GenotypeConcordance tool
Merge pull request #104 from broadinstitute/gg_add_specificity_to_genotype_concordance

Add new statistic 'Specificity' to GenotypeConcordance tool
Remove some sun.reflect imports
Merge pull request #106 from broadinstitute/mds_remove_sun

Remove some sun.reflect imports