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jpayne@69
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1 -- Version history --
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jpayne@69
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2
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jpayne@69
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3 3.23 - Added -D and --banded option to nucmer. These options can be used to
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jpayne@69
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4 specify the largest indel that will be included in an alignment
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jpayne@69
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5 segment without breaking it in two pieces.
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jpayne@69
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6 3.22 - Significant 'dnadiff' bug fixes. Breakpoints, unaligned seqs, and
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jpayne@69
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7 SNP counts now reported accurately. Unaligned contig output format
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jpayne@69
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8 switched to match show-diff format. Dynamic memory allocation for
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jpayne@69
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9 run-mummer1. Turned off output of the near useless .cluster files
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jpayne@69
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10 from nucmer and promer (let us know if you still want them).
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jpayne@69
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11 3.21 - gcc compatability fix.
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jpayne@69
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12 3.20 - Added 'dnadiff' comparative analysis script, 'show-diff' nucmer
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jpayne@69
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13 utility, and fixed a number of build issues.
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jpayne@69
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14 3.19 - Fixed gcc4 build problem .
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jpayne@69
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15 3.18 - Fixed bugs in delta-filter, began migrating to delta library.
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jpayne@69
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16 3.17 - Many changes, major upgrade. Added/improved delta-filter, show-snps,
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jpayne@69
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17 mummerplot, and mgaps. Multiplot capability added to mummerplot.
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jpayne@69
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18 3.16 - Added 'delta-filter' utility.
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jpayne@69
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19 3.15 - Fixed --nooptimize in nuc/promer.
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jpayne@69
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20 3.14 - Fixed gcc3 compilation bug.
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jpayne@69
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21 3.13 - Added -d, -g, -G and -o options to show-coords and updated
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jpayne@69
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22 documentation. Fixed bug in show-tiling -R.
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jpayne@69
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23 3.12 - Added the --nosimplify option to nucmer for repeat searching. Fixed
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jpayne@69
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24 a bug in nucmer and promer. Fixed rounding issue in show-coords.
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jpayne@69
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25 Updated citations.
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jpayne@69
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26 3.11 - Fixed bug show-tiling -R option. Added some mapview changes. Fixed
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jpayne@69
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27 the issue with mummerplot being to faint.
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jpayne@69
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28 3.10 - Now Mac OSX compatible. Added -R option to show-tiling.
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jpayne@69
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29 3.08 - Added MUMmer examples web docs which gives brief walkthroughs.
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jpayne@69
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30 3.07 - Added the 'mapview' plotting utility and appropriate documentation.
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jpayne@69
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31 Fixed origin wrap shadowing bug in show-tiling when using the -c option.
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jpayne@69
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32 NUCmer and PROmer now convert to absolute paths to avoid ambiguity.
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jpayne@69
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33 3.06 - Added -F and -h option to mummer. Changed -mumcand option to
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jpayne@69
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34 -mumreference, but left deprecated -mumcand option available. Added
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jpayne@69
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35 -maxmatch option to mummer, and changed default behavior of all
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jpayne@69
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36 applicable programs to -mumreference (nucmer, promer and mummer).
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jpayne@69
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37 Added -w (screen width) option to show-aligns. Updated documentation
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jpayne@69
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38 with all of these changes.
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jpayne@69
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39 3.05 - Added -k option to show-coords to only display the best frame for
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jpayne@69
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40 overlapping PROmer alignments. Added --[no]optimize option to nucmer
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jpayne@69
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41 and promer to allow alignment score optimization to be turned off, i.e
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jpayne@69
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42 allow alignments to extend to the ends of sequences rather than
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jpayne@69
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43 backtracking to optimize the alignment score. Updated docs.
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jpayne@69
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44 3.04 - Fixed combineMUMs bug and added new option, added some developer
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jpayne@69
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45 support in the src/kurtz subdirectory, and added extra INSTALL
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jpayne@69
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46 information in the docs.
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jpayne@69
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47 3.03 - Added HTML user manual in the /docs/htmlmanual/ subdir.
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jpayne@69
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48 3.02 - Fixed small bug in show-coords. Added additional options
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jpayne@69
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49 to show-coords. Added extra help text to show-tiling. Changed
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jpayne@69
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50 contact email address. Consistent padding added to combineMUMs.
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jpayne@69
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51 3.01 - Fixed off-by-one error in multi-reference 'mummer' usage.
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jpayne@69
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52 3.00 - Initial open source release!
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