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Created with Raphaël 2.2.027May2621191816151412111287423Apr201713430Mar115225Feb23222117161311527Jan2625201611109872131Dec302922211918177652128Nov262524201918171614111097654331Oct292827159818Sep17752116Aug1526Jul2411743218Jun529May232221169876130Apr292524232217161497525Mar2120191864128Feb27231910986532131Jan2723222120131110987543219Dec1817161513121196425Nov181413126229Oct2714119328Sep27262524231913111024Aug231615141328Jun271130May30Apr3226Mar21632112Feb3129Jan2827262524161514927Dec261918161312119825Nov14543231Oct302922111018Sep1731Aug30242214824JulRemoved accidental copy in BinTree to fix speedadd note about CLI change for coverageupdate the help for coverage to reflect new role of A versus B.update coverage docstweak testonly set end to 1 if slop is negative and rolls off start of chromMerge pull request #243 from nkindlon/masterAddressed BinTree memory blow-up; -m in fisher (w/ unit tests)Merge pull request #242 from gtamazian/getfasta-fixesShow warning if a FASTA index file is outdatedTests for IUPAC processing fixedMerge pull request #239 from nkindlon/masterFixed build break in CommonHelpFixed 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/master