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Created with Raphaël 2.2.018May16151412111287423Apr201713430Mar115225Feb23222117161311527Jan2625201611109872131Dec302922211918177652128Nov262524201918171614111097654331Oct292827159818Sep17752116Aug1526Jul2411743218Jun529May232221169876130Apr292524232217161497525Mar2120191864128Feb27231910986532131Jan2723222120131110987543219Dec1817161513121196425Nov181413126229Oct2714119328Sep27262524231913111024Aug231615141328Jun271130May30Apr3226Mar21632112Feb3129Jan2827262524161514927Dec261918161312119825Nov14543231Oct302922111018Sep1731Aug30242214824Jul23Fixed some merge errorsFixed sample unit testforgot b.bed in coverage unit testsforgot a.bed in unit tests for coverageChanged help in all tools to use common helpmerge conflictMerge branch 'jmarshall-warnings3'merge conflictsjmarshall-warni…jmarshall-warnings3fix help to reflect interface changemerge cleanupcleanupMerge pull request #225 from nkindlon/masterUnit tests for coverge, corrections to -split behavior for jaccard and fisher, minor code clean upFixed BedPlus bug, now only requires first 3 fields instead of 6Merge pull request #231 from yanlinlin82/masterMinor makefile improvmentsMerge branch 'master' of https://www.github.com/nkindlon/bedtools2first check in for new coverage toolFix a crash bug (when end == -1).Avoid overflow in int2str()Move "using namespace std" after #includesFixed bug where name conventions weren't tested for unsorted data; stopped namecheck on unmapped bam recordsForgot unit test directory for spacing.forgot src/utils/ToolBase directoryfirst check in for mass refactor from program to tools APIcorected unit test files for VCF insertions; changed to min instead of max for SV's with multiple valsMerge pull request #224 from nkindlon/masterMerge branch 'master' of https://github.com/nkindlon/bedtools2Fixed bug 223, Insertions for VCF records. Added unit test.Merge pull request #222 from nkindlon/masterCorrected bug 218 by disabling intra-file name convention checking and allowing -nonamecheck for unsorted filesMerge pull request #219 from lindenb/sortOnRefsort BED on faidx filefix merge docs on how to report strand with . Thanks to @balwierz.Merge branch 'master' of https://github.com/arq5x/bedtools2add tests for getfastarevcomp support for IUPACMerge pull request #204 from nkindlon/masterChanged -nonamecheck to warning only, added to help for map, closest, jaccardAddressed bug #208; seg fault when VCF doesn't have SVLEN for imprecise variants.