Add bgzip build
Add Tabix source
Add building of tabix source
Update Multi.pm to use  for directory for temp run scripts, and update align.pl to specify that value.  Move the configuration regression tests to a regression directory.  Add .gitignore for tabix
Update align test validation to ignore new jobfiles directory
Add Copyright info
Update umake/gotcloud to shift the return code from system calls
snpcall - add validation that the BAMs in the index exist for the steps that need them
umake filters - ensure the minDP/maxDP are whole numbers and not fractions
Upgraged BWA version
Remove older version of BWA
Upgrade to current libStatGen to bring in secondary flag logic
Upgrade bamUtil so dedup & recab can ignore secondary reads
Upgrade qplot to the latest version that ignores secondary reads
Merge in current bamUtil
Update metrics with new dedup/recab
Add BWA_MEM as an option for gotcloud align
Fix typo in debian/rules.bin
version 1.11a
Align - write timestamps to the Makefile log as each step is started/done