Update samtools index to return an error code if it fails to build the index
Add premo for pre-Mosaik processing
Add premo to the Makefile
Update premo.cpp to add unistd.h include for rmdir
Merge branch 'master' of github.com:statgen/gotcloud
merge latest bamUtil
Mosaik - add premo step to get mfl (median fragment length)
align TEST - Update expected results since mergeBam now has the --ignorePI flag
gotcloud - allow it to be in a bin/gotcloud/ subdirectory
snpcall use uncompressed BAMs for calmd
snpcall add check to ensure BAMs are not empty.
Fix ALIGN - wasn't creating .done for bwa-mem step
Merge latest libStatGen
Merge bamUtil phonehome
Merge latest libStatGen
Merge from Master
update phonehome url