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Created with Raphaël 2.2.024Jul2321201817326Jun198623May20151426Apr230Mar2013119628Feb242321191817161513121187530Jan2928272624231816121085231Dec3029211713128729Nov282517161587432126Oct25242111730Sep2827232216151310865131Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110876543130Dec29201826Nov251918numpy for rtdnumpy for rtdreorg for rtdadd setup.py. for venvadd pip reqs. in hopes of mpl support on rtdadd pip reqs. in hopes of mpl support on rtdtrying to suppor mpltrying to suppor mplremove redundancy in conf.pyadd 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_fix