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50 most recent check-ins
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2024-12-07
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| 23:49 | README: explain we've moved to github Leaf check-in: 7cb4f16b4a user: gav tags: trunk | |
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2024-12-02
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| 13:47 | translatorator: avoid duplicate sequence names in fasta output. check-in: 8d197c599d user: iws573 tags: trunk | |
| 13:47 | DelimitedStatSink: make sure and write header line even if no lines are written. check-in: 18b6a8909c user: iws573 tags: trunk | |
| 13:46 | count-trailing-kmers: fix check-in: 06686214cc user: iws573 tags: trunk | |
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2024-11-29
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| 11:23 | translatorator: when summarising, only take alignments with high identity to avoid overestimating cluster proportions. check-in: 72b487fc79 user: gav tags: trunk | |
| 00:17 | translatorator: fix aa sequence summary check-in: 8beee8d16c user: iws573 tags: trunk | |
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2024-11-28
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| 23:16 | Translatorator: whoops, fix again. check-in: b76b12caa0 user: gav tags: trunk | |
| 22:49 | Translatorator: implement -only-translatable, and also fix aa output when it's not turned on check-in: 665bd0f935 user: gav tags: trunk | |
| 17:13 | translatorator: make -dna-fasta and -aa-fasta work. check-in: 53078f17e1 user: gav tags: trunk | |
| 17:08 | translatorator: fixes check-in: 82d9ad72ff user: iws573 tags: trunk | |
| 16:22 | Update copyright check-in: 340df5e4ab user: gav tags: trunk | |
| 09:42 | translatorator: add -fasta and -summary check-in: 66bb14f045 user: gav tags: trunk | |
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2024-11-15
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| 16:50 | translatorator: add -min-fraction-per-sample check-in: 282f38391d user: iws573 tags: trunk | |
| 00:10 | translatorator fixes check-in: 4f2cf7f183 user: iws573 tags: trunk | |
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2024-11-14
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| 22:37 | Translatorator: add clustering option. check-in: 5dede6fd42 user: gav tags: trunk | |
| 22:37 | WFAAligner: Use const& instead of & in function signatures check-in: 24f0bcaf84 user: gav tags: trunk | |
| 16:19 | Translatorator fixes check-in: 34c846b6de user: gav tags: trunk | |
| 14:37 | Translatorator: support FASTA as well as BAM/SAM/CRAM check-in: 5901b33e19 user: gav tags: trunk | |
| 14:37 | Fix comment about SSW check-in: 45f112c5a8 user: gav tags: trunk | |
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2024-11-06
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| 23:03 | Added genfile::translate() check-in: da708f5662 user: gav tags: trunk | |
| 22:51 | Added translatorator check-in: b631063e57 user: gav tags: trunk | |
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2024-08-22
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| 14:19 | Also fix translation of GAG (Glutamic Acid) amino acids check-in: 8ed648c50f user: gav tags: trunk | |
| 14:06 | Fix translation of GAA (Glutamic Acid) amino acids check-in: 01cc9a3761 user: gav tags: trunk | |
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2024-02-04
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| 22:52 | GeneView.js: alter aa colouring. check-in: 17f226a5c0 user: gav tags: trunk | |
| 22:39 | Fix reverse-orientation CDS boundaries again. check-in: 58042b8b30 user: gav tags: trunk | |
| 19:03 | Added zoomsa test files with genes and amino acids. check-in: 06975217c1 user: gav tags: trunk | |
| 19:02 | Fix Geneview amino acids for non-multiple-of-3 case. Improve aa display. check-in: 5804dbac44 user: gav tags: trunk | |
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2024-02-02
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| 10:40 | count-trailing-kmers: use multimap, not map to get counts right, and output better info. check-in: 69856af350 user: iws573 tags: trunk | |
| 10:37 | count-trailing-kmers: add -remove-trailing-homopolymers removal option, add -incl-read-ids option. check-in: 8bfa592d1c user: gav tags: trunk | |
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2024-01-29
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| 22:19 | count-trailing-kmers: add homopolymer compression option check-in: a56919c3a9 user: gav tags: trunk | |
| 22:16 | count-trailing-kmers: bugfixes check-in: e0a98f874d user: iws573 tags: trunk | |
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2024-01-26
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| 12:18 | Add count-trailing-kmers check-in: 9c58ab65f3 user: gav tags: trunk | |
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2024-01-08
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| 10:03 | zoomsa: Give gene view elemtns a data ID, to avoid removing the wrong ones. check-in: d15a561c89 user: gav tags: trunk | |
| 09:03 | Rename seemsa.cpp -> zoomsa.cpp check-in: eeeed09642 user: gav tags: trunk | |
| 09:00 | seemsa: rename to zoomsa. gene view fixes check-in: defe0773b8 user: gav tags: trunk | |
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2024-01-07
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| 12:19 | seemsa: gene view, fix rounding of coordinates when mapping from physical to sequence coords. check-in: 814e04904a user: gav tags: trunk | |
| 10:35 | Tweak amino acid view. check-in: 7338a5cfbf user: gav tags: trunk | |
| 00:47 | seemsa: call it seemsa again, for now. check-in: 9515326cd1 user: gav tags: trunk | |
| 00:46 | Gene view tweak check-in: cad2dff189 user: gav tags: trunk | |
| 00:43 | seemsa: gene view performance improvement check-in: 72f73f9443 user: gav tags: trunk | |
| 00:40 | seemsa: implement amino acids in genes. check-in: b7ab74df1f user: gav tags: trunk | |
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2024-01-03
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| 22:30 | seemsa: visual tweaks check-in: 967394f2fa user: gav tags: trunk | |
| 18:03 | seemsa: add bookmark? button and make history work. check-in: aee5e9167a user: gav tags: trunk | |
| 15:06 | seemsa: show CDS as well as exons. check-in: 2ef24cade0 user: gav tags: trunk | |
| 15:05 | seemsa: remove unwanted debug statements check-in: ac1ceebf43 user: iws573 tags: trunk | |
| 15:04 | assess-qualities: count N bases check-in: 1c9f4eac34 user: iws573 tags: trunk | |
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2024-01-02
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| 18:26 | Seemsa: add simple sequence compression. check-in: 92514041e5 user: gav tags: trunk | |
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2024-01-01
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| 16:13 | Fix zoom in lines, don't draw out-of-view reference sequence bases check-in: 3fcdaf6cec user: gav tags: trunk | |
| 15:38 | seemsa: Don't update state. Show base names when zoomed in. check-in: ff07f9e818 user: gav tags: trunk | |
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2023-12-23
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| 18:24 | seemsa: implement simple form of sequence decompression (allow numbers of bases to copy from the 1st sequence) in MSAView.js. A TODO is to implement the corresponding compression in seemsa.cpp check-in: b6ec3a577a user: gav tags: trunk | |