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authorcube <cube@pkgsrc.org>2004-12-05 15:24:54 +0000
committercube <cube@pkgsrc.org>2004-12-05 15:24:54 +0000
commit7e470db80be2798a0870a43a49b48030635e2e83 (patch)
treef93522af3947f7c375a4e1f6158aa253be3b8a64 /x11
parent59c35abe3d95e8e27d327b855be5b70d65e60d34 (diff)
downloadpkgsrc-7e470db80be2798a0870a43a49b48030635e2e83.tar.gz
Update to version 3.15. From David Price in PR#28305.
3.05 - Added -k option to show-coords to only display the best frame for overlapping PROmer alignments. Added --[no]optimize option to nucmer and promer to allow alignment score optimization to be turned off, i.e allow alignments to extend to the ends of sequences rather than backtracking to optimize the alignment score. Updated docs. 3.06 - Added -F and -h option to mummer. Changed -mumcand option to -mumreference, but left deprecated -mumcand option available. Added -maxmatch option to mummer, and changed default behavior of all applicable programs to -mumreference (nucmer, promer and mummer). Added -w (screen width) option to show-aligns. Updated documentation with all of these changes. 3.07 - Added the 'mapview' plotting utility and appropriate documentation. Fixed origin wrap shadowing bug in show-tiling when using the -c option. NUCmer and PROmer now convert to absolute paths to avoid ambiguity. 3.08 - Added MUMmer examples web docs which gives brief walkthroughs 3.10 - Now Mac OSX compatible. Added -R option to show-tiling. 3.11 - Fixed bug show-tiling -R option. Added some mapview changes. Fixed the issue with mummerplot being to faint. 3.12 - Added the --nosimplify option to nucmer for repeat searching. Fixed a bug in nucmer and promer. Fixed rounding issue in show-coords. Updated citations. 3.13 - Added -d, -g, -G and -o options to show-coords and updated documentation. Fixed bug in show-tiling -R 3.14 - Fixed gcc3 compilation bug 3.15 - Fixed --nooptimize in nuc/promer.
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