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Created with Raphaël 2.2.031Dec3029211713128729Nov282517161587432126Oct25242111730Sep2827232216151310865131Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120191521Sep17151428Aug22Jul25Jun1529May1912116528Apr272624232221159interface tweaks.interface tweakAdded groupby back into the bedtools package.added cluster tool. both cluster and merge require sorted files for efficiency.Relax pairing req's for bamtobed and pairtobedMissing include.added version to subcommandsWarn only when requested chrom not in FASTA file.Added makewindows sub-commandHandle mutiple UCSC header lines and mid-file headers/comments.uBG and mIB use new Point class.Change shuffleBed defaults.Makefile mod.updated to bamtools 2.0wipe away bamtoolsshuffleBed now weights by chrom size by def.banner, include.newline at end of fileImprovements to CLI.fixUses C++ string comp. Thx to @jmarshall. to for compat. thx to @jmarshallremove superfluous *.oremove superfluous *.ogussygussygussyacknowledge heng li.tweaked menu.tweaked menu.New svn/git/samtools - like bedtools interface.Removed most version.h includes from sub-tools.First pass at new, consolidated CLI.preliminarymakefile tweakComment fix.Further nullBed tweaking.return true on BLANKRemoved nullBed nonsense.bamToBed -bedpe now handles singletons.