ChangeLog

-- Version history --

3.23 - Added -D and --banded option to nucmer. These options can be used to
       specify the largest indel that will be included in an alignment
       segment without breaking it in two pieces.
3.22 - Significant 'dnadiff' bug fixes. Breakpoints, unaligned seqs, and
       SNP counts now reported accurately. Unaligned contig output format
       switched to match show-diff format. Dynamic memory allocation for
       run-mummer1. Turned off output of the near useless .cluster files
       from nucmer and promer (let us know if you still want them).
3.21 - gcc compatability fix.
3.20 - Added 'dnadiff' comparative analysis script, 'show-diff' nucmer
       utility, and fixed a number of build issues.
3.19 - Fixed gcc4 build problem	.
3.18 - Fixed bugs in delta-filter, began migrating to delta library.
3.17 - Many changes, major upgrade. Added/improved delta-filter, show-snps,
       mummerplot, and mgaps. Multiplot capability added to mummerplot.
3.16 - Added 'delta-filter' utility.
3.15 - Fixed --nooptimize in nuc/promer.
3.14 - Fixed gcc3 compilation bug.
3.13 - Added -d, -g, -G and -o options to show-coords and updated
       documentation. Fixed bug in show-tiling -R.
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.
3.11 - Fixed bug show-tiling -R option. Added some mapview changes. Fixed
       the issue with mummerplot being to faint.
3.10 - Now Mac OSX compatible. Added -R option to show-tiling.
3.08 - Added MUMmer examples web docs which gives brief walkthroughs.
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.
3.06 - 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.	
3.05 - 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.
3.04 - Fixed combineMUMs bug and added new option, added some developer
       support in the src/kurtz subdirectory, and added extra INSTALL
       information in the docs.
3.03 - Added HTML user manual in the /docs/htmlmanual/ subdir.
3.02 - Fixed small bug in show-coords. Added additional options
       to show-coords. Added extra help text to show-tiling. Changed
       contact email address. Consistent padding added to combineMUMs.
3.01 - Fixed off-by-one error in multi-reference 'mummer' usage.
3.00 - Initial open source release!