Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/ChangeLog @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 67:0e9998148a16 | 69:33d812a61356 |
|---|---|
| 1 -- Version history -- | |
| 2 | |
| 3 3.23 - Added -D and --banded option to nucmer. These options can be used to | |
| 4 specify the largest indel that will be included in an alignment | |
| 5 segment without breaking it in two pieces. | |
| 6 3.22 - Significant 'dnadiff' bug fixes. Breakpoints, unaligned seqs, and | |
| 7 SNP counts now reported accurately. Unaligned contig output format | |
| 8 switched to match show-diff format. Dynamic memory allocation for | |
| 9 run-mummer1. Turned off output of the near useless .cluster files | |
| 10 from nucmer and promer (let us know if you still want them). | |
| 11 3.21 - gcc compatability fix. | |
| 12 3.20 - Added 'dnadiff' comparative analysis script, 'show-diff' nucmer | |
| 13 utility, and fixed a number of build issues. | |
| 14 3.19 - Fixed gcc4 build problem . | |
| 15 3.18 - Fixed bugs in delta-filter, began migrating to delta library. | |
| 16 3.17 - Many changes, major upgrade. Added/improved delta-filter, show-snps, | |
| 17 mummerplot, and mgaps. Multiplot capability added to mummerplot. | |
| 18 3.16 - Added 'delta-filter' utility. | |
| 19 3.15 - Fixed --nooptimize in nuc/promer. | |
| 20 3.14 - Fixed gcc3 compilation bug. | |
| 21 3.13 - Added -d, -g, -G and -o options to show-coords and updated | |
| 22 documentation. Fixed bug in show-tiling -R. | |
| 23 3.12 - Added the --nosimplify option to nucmer for repeat searching. Fixed | |
| 24 a bug in nucmer and promer. Fixed rounding issue in show-coords. | |
| 25 Updated citations. | |
| 26 3.11 - Fixed bug show-tiling -R option. Added some mapview changes. Fixed | |
| 27 the issue with mummerplot being to faint. | |
| 28 3.10 - Now Mac OSX compatible. Added -R option to show-tiling. | |
| 29 3.08 - Added MUMmer examples web docs which gives brief walkthroughs. | |
| 30 3.07 - Added the 'mapview' plotting utility and appropriate documentation. | |
| 31 Fixed origin wrap shadowing bug in show-tiling when using the -c option. | |
| 32 NUCmer and PROmer now convert to absolute paths to avoid ambiguity. | |
| 33 3.06 - Added -F and -h option to mummer. Changed -mumcand option to | |
| 34 -mumreference, but left deprecated -mumcand option available. Added | |
| 35 -maxmatch option to mummer, and changed default behavior of all | |
| 36 applicable programs to -mumreference (nucmer, promer and mummer). | |
| 37 Added -w (screen width) option to show-aligns. Updated documentation | |
| 38 with all of these changes. | |
| 39 3.05 - Added -k option to show-coords to only display the best frame for | |
| 40 overlapping PROmer alignments. Added --[no]optimize option to nucmer | |
| 41 and promer to allow alignment score optimization to be turned off, i.e | |
| 42 allow alignments to extend to the ends of sequences rather than | |
| 43 backtracking to optimize the alignment score. Updated docs. | |
| 44 3.04 - Fixed combineMUMs bug and added new option, added some developer | |
| 45 support in the src/kurtz subdirectory, and added extra INSTALL | |
| 46 information in the docs. | |
| 47 3.03 - Added HTML user manual in the /docs/htmlmanual/ subdir. | |
| 48 3.02 - Fixed small bug in show-coords. Added additional options | |
| 49 to show-coords. Added extra help text to show-tiling. Changed | |
| 50 contact email address. Consistent padding added to combineMUMs. | |
| 51 3.01 - Fixed off-by-one error in multi-reference 'mummer' usage. | |
| 52 3.00 - Initial open source release! |