1. Preliminary release of the chrom_sweep algorithm.
New options
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1. genomeCoverageBed no longer requires a genome file when working with BAM input. It instead uses the BAM header.
2. tagBam now has a -score option for annotating alignments with the BED "scores" field in annotation files. This overrides the default behavior, which is to use the -labels associated with the annotation files passed in on the command line.
Bug fixes
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1. Correct a bug that prevented proper BAM support in intersectBed.
2. Improved detection of GFF features with negative coordinates.