Subject: CVS commit: pkgsrc/biology/mummer
To: None <>
From: Quentin Garnier <>
List: pkgsrc-changes
Date: 12/05/2004 15:24:54
Module Name:	pkgsrc
Committed By:	cube
Date:		Sun Dec  5 15:24:54 UTC 2004

Modified Files:
	pkgsrc/biology/mummer: Makefile PLIST distinfo
	pkgsrc/biology/mummer/patches: patch-aa

Log Message:
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.

To generate a diff of this commit:
cvs rdiff -r1.3 -r1.4 pkgsrc/biology/mummer/Makefile
cvs rdiff -r1.1.1.1 -r1.2 pkgsrc/biology/mummer/PLIST \
cvs rdiff -r1.1.1.1 -r1.2 pkgsrc/biology/mummer/patches/patch-aa

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.