wanted to remove excludesuffix=_text,_notes so that those types of strings
would still get parsed from the clinical xml files, and replaced it with
excludesuffix=_aaaa,_zzzz
lots of clean-up in this code ... there were still a few spots where
things were case sensitive and it was a bit harder to clean those up
than I first thought it was going to be ... hopefully this is all
taken care of now
this was not working quite correctly if the two input feature matrices
had barcodes of different lengths (which were still referring to the same
tumor samples), and also in the case where a CNVR feature did not have
a genomic coordinate (because it was a gene-level feature provided by
the Broad and failed to be annotated)
modified this so that the output will have the same order as the input
(white) list(s) of features
modified the call to tsvIO.writeTSV_dataMatrix just to make things more explicit
added options to writeTSV_dataMatrix to write out the matrix with specified
row- or column-order, and also the option to write out "simple" feature names
fixed a bug in a debug print statement
added an additional debug print statement if any of these top-level programs
are called without the correct command-line arguments