1. Fixed bug that caused some GFF files to be misinterpreted as VCF. This prevented the detection of overlaps.
2. Added a new "-tag" option in bamToBed that allows one to choose the _numeric_ tag that will be used to populate the score field. For example, one could populate the score field with the alignment score with "-tag AS".
3. Updated the BamTools API.
Version 2.8.2 (July-18-2010)
1. Fixed a bug in bedFile.h preventing GFF strands from being read properly.
2. Fixed a bug in intersectBed that occasionally caused spurious overlaps between BAM alignments and BED features.