06d7be056190c14b85e71bc12523f18ea6815b5e
markd
  Mon Dec 7 00:50:29 2020 -0800
BLAT mmap index support merge with master

diff --git src/utils/bedFixBlockOverlaps src/utils/bedFixBlockOverlaps
index eb009b4..46786fd 100755
--- src/utils/bedFixBlockOverlaps
+++ src/utils/bedFixBlockOverlaps
@@ -1,54 +1,55 @@
 #!/usr/bin/env python
 
 import logging, sys, optparse
 from collections import defaultdict
 from os.path import join, basename, dirname, isfile
 
 # === COMMAND LINE INTERFACE, OPTIONS AND HELP ===
 parser = optparse.OptionParser("usage: %prog [options] filename - fix overlapping blocks in a bed file, produced e.g. by pslMap") 
 
 parser.add_option("-d", "--debug", dest="debug", action="store_true", help="show debug messages") 
 #parser.add_option("-f", "--file", dest="file", action="store", help="run on file") 
 #parser.add_option("", "--test", dest="test", action="store_true", help="do something") 
 (options, args) = parser.parse_args()
 
 if options.debug:
     logging.basicConfig(level=logging.DEBUG)
 else:
     logging.basicConfig(level=logging.INFO)
 # ==== FUNCTIONs =====
     
 # ----------- MAIN --------------
 if args==[]:
     parser.print_help()
     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))