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Created with Raphaël 2.2.026Jan24231816121085231Dec3029211713128729Nov282517161587432126Oct25242111730Sep2827232216151310865131Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120191521Sep17151428Aug22Jul25Jun1529May1912116528Apr272624232221159refactored intersect; better -bed support for split BAM alignmentsfixed util Makefiles to recompile when header changesfix typoadd ranlib to bamtools' makefile. thx to jphn marshallbail out early if no ivls in binadded count_distinct to groupbyBugfix: fix segfault when -t first or -t last used with -iu or -idAdd ignore options for features up- and down-stream of Abail early if not BEDs in BIN; revert to map from unordered_mapAdded isBed12 attr. and overlap fraction support for blocked intervals.Inform users that map reqs. sorted input. Update default.Inform users that merge reqs. sorted input.Fixed typo. Thanks @daler.Fixed help for groupby. Thanks @daler.First 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.