minor bug fixes

diff --git a/checkrmask.py b/checkrmask.py
index 99d74a50cdc3faec378b17070862ad90da99a954..457e4c1f9ebedb7b4daf6137f9f8b850635afb28 100755 (executable)
--- a/checkrmask.py
+++ b/checkrmask.py
@@ -192,7 +192,7 @@ def checkrmask(dbfile, filename, outFileName, goodFileName, startField=0, cacheP
             outfile.write(outline + "\n")
 
         if len(finalresults) == 0:
-            outline = "%s\tNR\tNR\t%0.00" % line
+            outline = "%s\tNR\tNR\t0.00" % line
             print outline
             outfile.write(outline + "\n")
 
@@ -201,4 +201,4 @@ def checkrmask(dbfile, filename, outFileName, goodFileName, startField=0, cacheP
 
 
 if __name__ == "__main__":
-    main(sys.argv)
\ No newline at end of file
+    main(sys.argv)

diff --git a/distalPairs.py b/distalPairs.py
index be403109110c3fb40f7bba831f6c2ea48e496536..dc836501c6b2b98f53b5a4a84ce8778c9673a1a7 100755 (executable)
--- a/distalPairs.py
+++ b/distalPairs.py
@@ -147,13 +147,15 @@ def addSplicesToUniqReads(RDS, uniqDict):
     for readID in splicesDict:
         theRead = splicesDict[readID]
         read0 = theRead[0]
-        del read0[1]
+        read0["start"] = read0["startL"]
+        del read0["stopL"]
         try:
             uniqDict[readID].append(read0)
         except:
             if len(theRead) == 4:
                 read2 = theRead[2]
-                del read2[1]
+                read2["start"] = read2["startL"]
+                del read2["stopL"]
                 uniqDict[readID] = [read0,read2]
 
 

diff --git a/makewiggle.py b/makewiggle.py
index 7440a796f73038130abb89ef593df425ac2921f6..139924e10f51642bfd02603213516f234fc547ea 100755 (executable)
--- a/makewiggle.py
+++ b/makewiggle.py
@@ -115,6 +115,7 @@ def makewiggle(name, hitfilename, outfilename, doNormalize=True, color=None, alt
     if limitChrom is not None:
         chromLimit = True
 
+    groupName = ""
     if group:
         groupName = "group=%s" % group