[PATCH] Upgrade bedtools to 0.25.0.

[Ben Woodcroft]

A reasonably straightforward update.


Version 2.25.0 (3-Sept-2015)

1. Added new -F option that allows one to set the minimum fraction of overlap required for the B interval. This complements the functionality of the -f option.Available for intersect, coverage, map, subtract, and jaccard.
2. Added new -e option that allows one to require that the minimum fraction overlap is achieved in either A _OR_ B, not A _AND_ B which is the behavior of the -r option. Available for intersect, coverage, map, subtract, and jaccard.
3. Fixed a longstanding bug that prevented genomecov from reporting chromosomes that lack a single interval.
4. Modified a src directory called "aux" to "driver" to prevent compilation errors on Windows machines. Thanks very much to John Marshall.
5. Fixed a regression that caused the coverage tool to complain if BED files had less than 5 columns.
6. Fixed a variable overload bug that prevented compilation on Debian machines.
7. Speedups to the groupby tool.
8. New -delim option for the groupby tool.
9. Fixed a bug in map that prevented strand-specifc overlaps from being reported when using certain BEDPLUS formats.
10. Prevented excessive memory usage when not using pre-sorted input.

0001-gnu-bedtools-Update-to-2.25.0.patch
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