Interval List Tool:

added functionality so that tool can use a vcf as a source for intervals.
Fixed Faked Filter files.  Need them to be of size one element for the faked filter file to have the same number of elements as other faked types.
Merge pull request #117 from broadinstitute/gg_fixFakedFilterFiles

Fixed Faked Filter files.  ...
Various aesthetic tweaks for HTML doc generation.
Merge pull request #119 from broadinstitute/mds_fix_metrics_html

Various aesthetic tweaks for HTML doc generation.
Added read group tag option
Merge pull request #122 from rernst/SamToFastq_add_read_group_tag_option

Added read group tag option, resolves #108 #114
Added SAM/BAM/CRAM converter tests. This relies on the jc_cram_changes branch of the htsjdk.
SamReader conversion of Picard public.
Added common argument for reference fasta to support CRAM input/output.
Reference fasta should be optional.
Use SamReaderFactory makeDefault with reference sequence whenever possible to allow for CRAM support.
Code review changes.
Make parseOptionsFile public, with a little more control over behavior.
Merge pull request #125 from broadinstitute/aw_option_file_parse

Make parseOptionsFile public, with a little more control over behavior.
Code review changes.
Merge pull request #124 from broadinstitute/jc_cram_changes

Added SAM/BAM/CRAM converter tests. This relies on the jc_cram_changes b...
Update build.xml

Update picard to 1.127
removing explain-flags.html from master as it now lives in the gh-pages branch
Merge pull request #131 from broadinstitute/nh_remove_explain_flags_from_master

removing explain-flags.html from master as it now lives in the gh-pages ...
fix build based on commit 59b1e89e182b56eb7ae44ac09259862c88dd2650
Merge pull request #132 from broadinstitute/nh_fix_build_xml

fix build based on commit 59b1e89e182b56eb7ae44ac09259862c88dd2650
Merge pull request #105 from broadinstitute/yf_merge_VCF_to_IntervalList_and_ILTOOLS

Interval List Tool:
allow colors to be disabled with -Dpicard.cmdline.color_status=false
adding the --list-commands argument to the main command line, to list
all the commands available without formatting.