d0ab96bfa4307ef666f194cdd2bda05608972cd1
max
  Mon Nov 23 04:44:23 2020 -0800
trying to address a problem in bedFixBlockOverlaps that appears in the
uniprot otto pipeline. This is a hacky fix, but the problem only appears
in very unusual assemblies, not on any mammal. refs #25784

diff --git src/utils/bedFixBlockOverlaps src/utils/bedFixBlockOverlaps
index eb009b4..46786fd 100755
--- src/utils/bedFixBlockOverlaps
+++ src/utils/bedFixBlockOverlaps
@@ -24,31 +24,32 @@
     exit(1)
 
 filename = args[0]
 if filename=="stdin":
     ifh = sys.stdin
 else:
     ifh = open(filename)
 
 for line in ifh:
     row = line.rstrip("\n").split("\t")
     bSizes = [int(x) for x in row[10].strip(",").split(",")]
     bStarts = [int(x) for x in row[11].strip(",").split(",")]
     newLens = []
     newStarts = []
 
-    # go over blockLens/blockStarts and fix overlaps
-    pos = 0
+    lastEnd = 0
     for bs, bl in zip(bStarts, bSizes):
-        if pos>bs:
-            diff = pos-bs
-            bs = pos
+        #print("lastEnd, start, length", lastEnd, bs, bl)
+        if lastEnd!=0 and lastEnd>bs:
+            diff = lastEnd-bs
+            bs = lastEnd
             bl = bl-diff
-        pos += bl
+            #print("fixed to: lastEnd, start, length", lastEnd, bs, bl)
+        lastEnd= bs+bl
         newLens.append(str(bl))
         newStarts.append(str(bs))
     row[10] = ",".join(newLens)
     row[11] = ",".join(newStarts)
     print("\t".join(row))