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Created with Raphaël 2.2.017Dec13128729Nov282517161587432126Oct25242111730Sep2827232216151310865131Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120191521Sep17151428Aug22Jul25Jun1529May1912116528Apr272624232221159shuffleBed 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.Removed need for nullBed. clear() otherFields in GetNextBed().Added -header to sortBedUse new GetNextBed() interface. Redux.Use new GetNextBed() interface.rename tool to acvoid conflicts. s/overlap/getOverlapMakefile aborts on first error.Add'l comments.Comments for header logic.force ^chrom ^track and ^browser headers to only occur on the first line.Allow headers to start with "chrom"lineNum is now tracked privately.Merge branch 'read_write_headers'Added unstaged files.Added -header to intersect, window, closest, slop, flank.Fiex off-by-one in linksBed.