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Created with Raphaël 2.2.02Nov31Oct302922111018Sep1731Aug30242214824Jul2321201817326Jun198623May20151426Apr230Mar2013119628Feb242321191817161513121187530Jan2928272624231816121085231Dec3029211713128729Nov282517161587432126Oct25242111730Sep2827232216151310865131Aug24Jul19131165130Jun29282423221716151414Apr83129Mar221817103124Feb23167231Jan272521191413765323Dec21Nov4Oct21Sep318Aug1665425Jul232221181715146543130Jun29876May543229Apr2826221514131229Mar2322181715141210319Feb126228Jan2723191110added new jaccard tool. see PMID: 22693437add "first" and "last" as new groupby options80 charrefactor VCF auto-detection80 char width80 char width80 char widthavoid -hist overflowformattingtweak healp for -split. cheers to @brentp for the nice additionsupport for extracting blocked BED records in fastaFromBedMerge pull request #28 from brentp/getfastaallow - to be specified for stdout fastachange -exons to -split. add tests that make sense.start of test for -exons argerrant debugstart of allowing to get concatenated sequence of exonsmissing includePrefer list over vector chromsweep's cache. Huge performance increases80char cleanup of merge.clear closest list if an overlap in closeststandardize tag reporting for bamtobedMerge pull request #27 from nathanweeks/masterIf "tac" doesn't exist (e.g., on non GNU/Linux systems like OS X & other BSDs), emulate with sed '1!G;h;$!d' (from http://www.catonmat.net/blog/sed-one-liners-explained-part-one/)sockaddr_in and sockaddr_in6 are defined in netinet/in.h, which may or may not be included by arpa/inet.h (per POSIX.1-2008). Explicitly include netinet/in.h to compilation on FreeBSD 9.0.exit is inout BAM file is not foundMerge pull request #26 from brentp/groupby_headerlet groupby handle a header line (starting with "#") as do otherfix corner case in chrom sweep. addresses GC issue #141complement warns to stderr.send warning to stderr.remove commentMerge pull request #25 from brentp/groupby-columnsadd tests for groupbyuse TokenizeColumns in groupBy and add lineFileUtilities as dependency to Makefileadd TokenizeColumns functionextraneous tab for windowbed -ctry reqs fileadd pybedtools req. for docsadd plot_directive