Here's a program for converting bed file to junctions. can be cloned from Github.

usage ./bin/bedToJunction <filename>|<stdin>

suggested usage: bamtobed -i <bamfile> -cigar | ./bin/bedToJunction - > junction.bed
**** use <-> when using stdin
Needed a bed file with cigar string
output file contains six columns:
	      column 1:        chromosome name
		  column 2:        junction start position (0-base start pos)
		  column 3:        junction end position (0-base start pos)
		  column 4:        name (ordered by chrom)
	      column 5:        number of reads supporting
	      column 6:        strand [+/-]