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Created with Raphaël 2.2.016Jan121085231Dec3029211713128729Nov282517161587432126Oct25242111730Sep2827232216151310865131Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120191521Sep17151428Aug22Jul25Jun1529May1912116528Apr272624232221159First cut at BlockedIntervals class to cleanup spliced BAMs and BED12Clearer desc. of mapBed's func. programming originsAdd stdint.hAdd stdint.hENH: groupBy now uses VectorOpsadd map/mapBed to scriptsUse updated chromsweep in intersect and map.Use -f and -r directly in chromsweepadded mode and antimode to VectorOpsAdded new ops to mapBedAdded new VectorOps class.first basic cut at mapBedstore all input fields and the indices of "extra" fields.overhaul of overlap interface. use allHits() and anyHits().enh: support for remote [ftp|http] fileschanged return codes.interface 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 *.o