4917a38c21a998a5f9710bb99b6d6e53f354c722
chmalee
  Thu Oct 19 12:03:21 2017 -0700
Only check overlap with the gap table if we are not checking the gap table. Only check unbridged gaps if explicitly asked

diff --git src/utils/qa/runBits src/utils/qa/runBits
index aee0421..2fc3c37 100755
--- src/utils/qa/runBits
+++ src/utils/qa/runBits
@@ -31,21 +31,23 @@
     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:
         gapOverlapOut = checkGapOverlap.checkGapOverlap(db, table, checkUnbridged)
 
     print output + gapOverlapOut
 
 if __name__ == "__main__":
     main()