Fix bed2interval from 0-base bed to 1-base interval

From the Picard javadoc:
http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html

Interval files are 1-based whereas BED files are 0-based
Merge pull request #93 from kevyin/patch-1

Fix bed2interval from 0-base bed to 1-base interval
Added Kevin Ying to the contributors list.
Clean up FreeBayes, samtools and realignment steps to feed through standard provenance tracking
Disable call background usage in FreeBayes which needs additional testing
Fixing passing the names attribute to the aligners.
Retain some alignment attributes during merge.

Picard drops the reserveed alignment attributes from
some of the aligners unless you tell it to keep
the attributes. In particular, dropping XS causes
Cufflinks to complain. This saves all of the
attributes set by Tophat, which may not be optimal.
Fix for incorrect Type=Int, tags in latest FreeBayes which GATK will not handle as invalid VCF