MergeBam - update to ignore PG lines with duplicate IDs
Release 1.0.9 (skipping 1.0.8)
Fix Stats to not try to not try to process a record after it is out of the loop since the record might be invalid
splitBam - fix description of --noeof option
WriteRegion - add exclude/required flags
Ignore secondary reads for dedup and making the recalibration table.  Add ExplainFlags commnad
Dedup & Recab - also skip QC Failures - add excludeFlags parameters
Update ClipOverlap to have excludeFlags
Bam2FastQ - upgrade to add --merge option to generate interleaved files.
Make sub-program names case independant
Bam2FastQ update to open the input file before opening the output files, so if there is an error, the outputs aren't opened
Update test expected results to reflect removed line from libStatGen Parameters Status call.
Phonehome version 1
PhoneHome version 2, update parameter to --noPhoneHome and show it in the params print
MergeBam - add option to ignore the RG PI field when checking headers
Merge in changes from master
Merge in PhoneHome
Update Version to temp phonehome version
Merge latest phonehome
ClipOverlap : fix bug for readName sorted when a read is filtered due to flags & add sorting validation