7ec55fe7a016d7da941602e441ed242a8e241b24
max
  Mon Apr 8 07:59:45 2019 -0700
usage update to the maf converter, no redmine

diff --git src/utils/cancerMafToBigBed src/utils/cancerMafToBigBed
index 55c1bf5..5db043f 100755
--- src/utils/cancerMafToBigBed
+++ src/utils/cancerMafToBigBed
@@ -47,34 +47,38 @@
     "alcohol_intensity",
     "bmi",
     "years_smoked",
     "height"
 ]
 
 
 # field descriptions for the AS file
 fieldDescs = {
 
 }
 
 # ==== functions =====
 def parseArgs():
     " setup logging, parse command line arguments and options. -h shows auto-generated help page "
-    parser = optparse.OptionParser("""usage: %prog [options] inDir outBb - summarize GDC MAF files to bigBed
+    parser = optparse.OptionParser("""usage: %prog [options] inDir annotationFile exposureFile outBb - summarize GDC MAF files to bigBed
 
     inDir will be recursively searched for .maf.gz files. Their variants will be extracted, written to outBb
 
+    annotationFile and exposureFile are two .tsv files, both are distributed by the GDC.
+    See /hive/data/outside/gdc/pancan33-variants/annotations/ for the versions from Jan 2019
+
+
     """)
 
     parser.add_option("-d", "--debug", dest="debug", action="store_true", help="show debug messages")
     #parser.add_option("-f", "--file", dest="file", action="store", help="run on file") 
     #parser.add_option("", "--test", dest="test", action="store_true", help="do something") 
     (options, args) = parser.parse_args()
 
     if args==[]:
         parser.print_help()
         exit(1)
 
     if options.debug:
         logging.basicConfig(level=logging.DEBUG)
     else:
         logging.basicConfig(level=logging.INFO)