picard version 1.125

picard version 1.125
adding options to show only the header or only the records in ViewSam
Merge pull request #112 from broadinstitute/nh_view_sam_only_header_or_only_records

adding options to show only the header or only the records in ViewSam
Also strip the "/2" in FastqToSam when using STRIP_UNPAIRED_MATE_NUMBER
Merge pull request #113 from broadinstitute/nh_fastq_to_sam_also_strip_slash_two_for_unpaired

Also strip the "/2" in FastqToSam when using STRIP_UNPAIRED_MATE_NUMBER
Fixed error in FilterFileFaker.  The faked files that it created were not readable by our own software.   Added a test to catch this.
Added additional documentation, remove unused file reference
Merge pull request #115 from broadinstitute/gg_fixBadFakedFilterFiles

Fixed error in FilterFileFaker.
picard version 1.126

picard version 1.126
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.