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Created with Raphaël 2.2.024Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120191521Sep17151428Aug22Jul25Jun1529May1912116528Apr272624232221159fixed bug in shuffleBed when using -incl.The output of fastaFromBed is now in the order of the input -bed file.Fixed bug in shuffleBed incorrectly disallowing a lack of -incl and -excl.mergeBed complains when no names or scores are present for -nms and -scores.Added -score option to mergeBed and allowed duplicate names for -nms option.Fixed -wao and -wo in intersectBed for zero-length features.Version 2.11.2MergeBed now correctly handles a max distance "-d" parameter.Added complementBed.hcomplementBed now uses vector<bool> instead of vector<short>Version = 2.11.1Fixed a casting issue in slopBed.Added newline to BamIndex.hFixed issue #62. Incorrect start and end coordinates for BEDCOV structs.Updated RELEASE_HISTORY to reflect version 2.11.0Version 2.11Fixed issue #55: mergeBed now reports 1-based starts for GFF files. Also,gzstream Makefile now inherits compilation flags from master Makefile.Tweaked commenting in shuffleBed.Improvements to shuffleBed, including:Issue #50. SlopBed now adds percent-based slop to features with the -pct option.Added size() method to BED struct.Fixed reporting bug for zero-length overlaps.Tweaked fjoin reporting.Removed groupBy from the BEDTools distribution.Added support for zero length features (start = end, e.g. insertions in ref genome).Seeding shuffleBed with srand((unsigned)time(0)+(unsigned)getpid()); Thanks to Rob Long.Fixed Issue #60. Improved randomization granularity for shuffleBed.Fixed Issue #59.Playing with README.Playing with README.Playing with README.Playing with README.Playing with README.Playing with README.Revising README to README.rstMinor formatting in slopBed.cpp.Allowed 8 or 9 column GFF/GTF files. Many thanks to Michael Hoffman.Fixed casting issue in windowBed.AddWindow() that cuased slop positions to run off the end of the chromosome.Changed BamAlignmentSupportData from private to public.