made some modifications to how the copy-number and/or mutation features
are created and how the thresholding is done to decide which ones to keep
changed a couple of the fixed constants to potentially allow more
"hotpoints" to be created
minor modifications to how it chooses which firehose run to use, and
some fixes so that it doesn't get tripped up by non-standard directory
names
the major change is that the "merged Dx" is now created by this script,
the other minor change is that some values that were being set to "NO"
are now "NO_or_NA" because this distinction is not necessarily clear
at times ...
changed where the cluster password is being obtained from
      $TCGAFMP_CLUSTER_SCRATCH/config
to    $TCGAFMP_CLUSTER_HOMEGOLEMPW
changed where the cluster password is grabbed from
added new option to ignore the TCGA annotations manager
added a new option to ignore the TCGA annotations manager
added a new option to ignore the TCGA annotations manager
maded some changes to the function removeUninformativeKeys(allClinDict)
added TCGAFMP_CLUSTER_HOME for finding the cluster password
comment typo