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Created with Raphaël 2.2.016Nov1587432126Oct25242111730Sep2827232216151310865131Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120191521Sep17151428Aug22Jul25Jun1529May1912116528Apr272624232221159Makefile tweak.Added bedpeToBam MakefileChanges for CSHL course.Added methods to store and report file headers upon request.minorexplain the sorting criteria. it's odd thanks to STL PQ behavior.Merge branch 'cluster'Added r. layer's cluster algorithm -clusterbwa modebwa mode-novo option in bamToBedNo need to force chroms to be sorted. Avoid diff.s b/w chr1 and 1Updated banner and help for multiIntersectBed.Handle header lines for new version of GetNextBedUpdated version.Fixed include goof and correct empty coveragev2.14.2Correct GetNextBed file. Oops.Prep for 2.14.1Added number of and list of files with coverage to mIBFixed closestBed help help to be -io instead of -noForce sorting when using multiIntersectBedAdded new multiIntersectBed tool. New relase to follow.Removed debugging message.Missed update of closest B feature to right of A feature.commentsnucBed now obeys strand'Version 2.13.4Undo previous. Dumb.Tweaked closestBed help for -DMerge branch 'master' of github.com:arq5x/bedtoolsreserve space up front for chromsweepMerge pull request #9 from jakebiesinger/masterUser can specify one of three orientations (a,b,ref)Oops. Extra ;Fix typo in closestBed: -S for opposite strands, not -sAdded a signed distance option (-D) to closestBedchromsweep now obeys -s and -Schromsweep no longer overloads results p_q on chrom change.Tweaked Makefile for proper zlib inclusion