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Created with Raphaël 2.2.023Jul21201817326Jun198623May20151426Apr230Mar2013119628Feb242321191817161513121187530Jan2928272624231816121085231Dec3029211713128729Nov282517161587432126Oct25242111730Sep2827232216151310865131Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov25191816141327Oct232120add plotting to conf.pyintersect docsinclude htmladded docs/_build. working on plots via @dalerfirst cut at sphinx-based docsslightly better randomizationreset each bedpeno need for flanks to the left of chrom.startadded shuffle logic for BEDPEadded -A option to subtract entire interval when any overlapAllow user to force closest interval to have different name (-N)allow \# in chrom name, just not at beg. of line (header)typo.print bedpe record immediately after unpaired read.Inital screen for -split overlaps should include the full span of A_iallow uint32 or int32 -tagscatch missing chroms for mapped BAM alignments. warn, don't out_of_range()correct missing tab in annotate's headeronly write to bam if bam output req. with -vMerge pull request #22 from agordon/bugfix/bamtobed_non_existing_fileregression tests for -abam w/ [-c | -wao | -wo]BamToBed: properly fail on non-existing input files.-wo -wao -c with -abam force BED output. Thanks to @agordon.genome file drives BAM header order in bedtobamfix off-by-one error in calc. -d for closestprefer empty() over size()safely handle empty inputhandle unaligned BAMs with -vremove extraneous .ofixed logic bug in bedtobam's -bed12 mode.Merge pull request #20 from agordon/feature/makewindows_name_fixWindowMaker: bugfix with using "srcwinnum" + genomeSetting Release-Version v2.16.2support for bedtools existing somewhere other than PATHadd omitted test dirs for "make test"fiddle w/ Makefiletwiddle MakefileMakefile tweakSetting Release-Version v2.16.1Setting Release-Version v2.16.0