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Created with Raphaël 2.2.017Jun16151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120191521Sep17151428Aug22Jul25Jun1529May1912116528Apr272624232221159coverageBed links with bamtools1.0bedToBam links with bamtools1.0preliminary support for bamtools1.0 for bamToBed.New BamTools 1.0 project structure and MakefileAdded BamTools-Ancillary filesChanged newline to tab in bamToBed for -tag -bed12.Further tweak to UCSC mysql help.Fixed multi-line UCSC mysql query in the help for multiple tool. Thanks to Brent Pedersen\!Patched Assaf Gordon's tweaks to gCB.Tweaked header in nucBedheader and custom pattern search for nucBed. Thanks to Can Alkan.Added output description to nucBed helpImprovements to closestBed. Thanks to suggestions by Brent Pedersen, Ryan Layer, Assaf Gordon, Dan Webster.mergeBed now _always_ reports in BED format (i.e., zero-based starts), regardless of input type.Added -5, -3, -trackline, -trackopts, and -dz options to genomeCoverageBed. Many thanks to Assaf Gordon.First cut at nucBed - profiles DNA sequences defined by BED intervals.Tweaked Makefile and added notboth option to pairToPair.fastaFromBed warns of exceeding length of chromosome and of zero length features.Updated version and RELEASE_HISTORY for 2.12.0Improved clarity for zero length features in coverageBed.Defaults to other constructors.Defaults for BED constructors. Cheers to John Marshall for the catch.logical, not operator. need coffee.Fixed overlflow error in pairToPairUnmapped BAM alignments are now captured by -v in intersectBed and windowBed. Thanks to Davide Cittaro.Removed Eclipse files.Corrected stranded logic for + features in flankBed.Updated flankBed helpAdded new flankBed tool.Tweaked an error message in genomeCoverageBed.Fixed bug in closestBed when B feature's end equal to A feature's start.Optionally set masking character (-mc) in maskFastaFromBed. Thanks to Can Alkan.Made bedToIgv filenames Windows friendly. Thanks to Jiam WangAdded option to report block number as score in bed12ToBed6fixed 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.