Add initial beagle4 support (not well tested) and fix ldrefine test check
Merge branch 'master' of github.com:statgen/gotcloud
development release 1.13.1
add missing beagle4 jar
align - ignore empty lines in the fastq index file as well as compress extra tabs and trim white space at the beginning or end of each field
libStatGen upgrade bgzf to version from GotCloud tabix
Add glfFlex source code
libVcf - error check for incorrect number of columns to print a friendly message rather than just a segmentation fault
align.pl, add warning messages when ignoring empty lines and extra space in the fastq index file
thunderVCF - fix exception when number of samples is 1
ldrefine, beagle, thunder - only run these pipelines if there are more than 1 sample
thunderVCF - make it a fatal error if thunderVCF is run on a single sample
indel - update pipeline to do mergebam as a separate step so it can be indexed for the genotype step.  Also, add an indel test
pipeline.pl - add error message if the configuration file is empty
pipeline.pl add FILELIST option to write files to a file rather than doing it as an ls runtime step since that will fail if it is too long.
snpcall - Replace glfMultiples and extract with glfFlex
Update umake test for glfFlex
Merge branch 'master' of github.com:statgen/gotcloud
Update ldrefine results now that glfFlex is used
umake test - add missing ped file to expected results