9ab0e5cc221ce3e6e0c19b50940eb0a24ea56243
max
  Thu Sep 25 01:22:04 2014 -0700
moving small tools into utils directory
diff --git src/oneShot/bedFixBlockOverlaps/bedFixBlockOverlaps src/oneShot/bedFixBlockOverlaps/bedFixBlockOverlaps
deleted file mode 100755
index 292d47d..0000000
--- src/oneShot/bedFixBlockOverlaps/bedFixBlockOverlaps
+++ /dev/null
@@ -1,54 +0,0 @@
-#!/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
-    for bs, bl in zip(bStarts, bSizes):
-        if pos>bs:
-            diff = pos-bs
-            bs = pos
-            bl = bl-diff
-        pos += bl
-        newLens.append(str(bl))
-        newStarts.append(str(bs))
-    row[10] = ",".join(newLens)
-    row[11] = ",".join(newStarts)
-    print "\t".join(row)
-
-
-