Revert "dont run phylop on inserts in leaves. they will just be 0 any…

…way"

(I changed my mind.  We want those zeros.  Keeping them allows us to have fewer headers, which can be a bigger win in terms of size of resulting wigs and bigwigs)
This reverts commit e789f92.

phyloP/halTreePhyloP.py

@@ -42,20 +42,14 @@ def computeTreePhyloP(args):
     bigwigCmds = []
     while len(visitQueue) > 0:
         genome = visitQueue.pop()
-        children = getHalChildrenNames(args.hal, genome)
         bedFlags = ""
         # Generate a bed file of all regions of 
         # genome that dont align to parent
         bedInsertsFile = outFileName(args, genome, "bed", "inserts", True)
         if genome != args.root:
-            if True or len(children) > 0:
-                runShellCommand(
-                    "halAlignedExtract %s %s --alignedFile %s --complement" % (
-                        args.hal, genome, bedInsertsFile))
-            else:
-                #empty file for leaves (ie we dont want to phyloP anything
-                #-- it all gets lifted down)
-                runShellCommand("rm -f %s && touch %s" % (bedInsertsFile, bedInsertsFile))
+            runShellCommand(
+            "halAlignedExtract %s %s --alignedFile %s --complement" % (
+                args.hal, genome, bedInsertsFile))
             bedFlags = "--refBed %s" % bedInsertsFile
 
         # Run halPhyloP on the inserts
@@ -91,6 +85,7 @@ def computeTreePhyloP(args):
             bigwigCmds.append(bwCmd)
 
         # Recurse on children.
+        children = getHalChildrenNames(args.hal, genome)
         for child in children:
             visitQueue.append(child)