bf6bfb867e296f780ca706f1203ae6d643cc5d52
chmalee
  Thu Oct 19 12:30:05 2017 -0700
woops still want to check overlaps unless gap table

diff --git src/utils/qa/runBits src/utils/qa/runBits
index 2fc3c37..2ff5fcd 100755
--- src/utils/qa/runBits
+++ src/utils/qa/runBits
@@ -1,53 +1,53 @@
 #!/usr/bin/env python2.7
 
 ##################################################################
 #
 #  05-24-17
 #  Matthew Speir
 #
 #  Run featureBits and check for overlap with gaps (including unbridged)
 #       
 ##################################################################
 
 import argparse
 
 from ucscGb.qa import qaUtils
 from ucscGb.qa.tables import checkGapOverlap
 
 def parseCommandLine():
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
         description='runs featureBits and checks for overlap with gaps.')
     parser.add_argument('db', type=str, help='the database to check')
     parser.add_argument('table', type=str, help='the name of a table to check')
     parser.add_argument('-u',"--checkUnbridged", default=False, action='store_true',
                         help='check for overlap with unbridged gaps')
     args = parser.parse_args()
 
     return args
 
 def main():
     args = parseCommandLine()
     db = args.db
     table = args.table
     checkUnbridged = args.checkUnbridged
 
     output = ""
 
     fbCmd = ["featureBits", "-countGaps", db, table]
     fbOut, fbErr = qaUtils.runCommand(fbCmd)
     output += "\n" + fbCmd[0] + " " + fbCmd[1] + " " + fbCmd[2] + " " + fbCmd[3] + "\n" + fbErr
 
     fbGapCmd = ["featureBits", "-countGaps", db, table, "gap"]
     fbGapOut, fbGapErr = qaUtils.runCommand(fbGapCmd)
     output += "\n" + fbGapCmd[0] + " " + fbGapCmd[1] + " " + fbGapCmd[2] + " " + fbGapCmd[3] +\
               " " + fbGapCmd[4] + "\n" + fbGapErr
 
     gapOverlapOut = ''
-    if checkUnbridged:
+    if table != 'gap':
         gapOverlapOut = checkGapOverlap.checkGapOverlap(db, table, checkUnbridged)
 
     print output + gapOverlapOut
 
 if __name__ == "__main__":
     main()