- 27 Mar, 2014 8 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
The threshold is a percentage, not a ratio.
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Mathieu Giraud authored
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Mathieu Giraud authored
('segmented.vdj.fa' may be not be the best filename choice, we should change it.)
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Mathieu Giraud authored
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Mathieu Giraud authored
'removeChevauchement' and possibly other infos
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- 26 Mar, 2014 2 commits
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Mikaël Salson authored
This is a file specific to each people. No reason for versioning
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Mikaël Salson authored
Because of the value for min_cover_representative that has changed (commit 4ee616a) the value computed in that case is now 4 instead of 5. So the representative is slightly longer which shifted the positions.
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- 25 Mar, 2014 1 commit
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Mikaël Salson authored
The library is now built in core, where we have the list of dependencies (dep.mk). Before dep.mk was in algo/ but the files it was refering to were in core/. Thus the dep.mk file was useless.
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- 26 Mar, 2014 11 commits
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Marc Duez authored
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Marc Duez authored
scatterplot.js : change methods to compute blobs radius, detect if blob represent a clone or a sequence and use correct size to compute radius
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Marc Duez authored
scatterplot.js : size analysis , detect if blob represent a clone/cluster or a window/sequence and use correct size
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Marc Duez authored
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Marc Duez authored
- delete select() function (use closure instead)
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Marc Duez authored
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Marc Duez authored
- clone mouseover have to work only on clone info and not on cluster info
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Marc Duez authored
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Marc Duez authored
used to know if we have to display only the representative of the cluster/clone or each windows/sequences
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Marc Duez authored
can now do the same for window/sequence
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- 25 Mar, 2014 16 commits
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
Now that a representative is almost always found, it is better to limit short examples to a small number of clones.
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Mathieu Giraud authored
This enables to have representatives even when setting -R to very small values. As a side effect, option -A should return representatives for every clone (-R is 1).
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Mikaël Salson authored
Changes in some sequences (in particular IGHV7-40*03) are responsible for those number changes. There is no such changes when using the previous germline dataset. For information IGHV7-40*03 changed from: >Z12320|IGHV7-40*03|Homo sapiens|P|V-REGION|1..291|289 nt|1| | | | |289+0=289|partial in 5'| | ctgcagctggtgcagtctgggcctgaggtgaagaagcctggggcctcagtgaaggtctcc tataagtcttctggttacaccttcaccatctatggtatgaattgggtatgatagacccct ggacagggctttgagtggatgtgatggatcatcacctacactgggaacccaacgtatacc cacggcttcacaggatggtttgtcttctccatggacacgtctgtcagcacggcgtgtctt cagatcagcagcctaaaggctgaggacacggccgagtattactgtgcga to: >AC241995|IGHV7-40*03|Homo sapiens|P|V-REGION|10101..10396|296 nt|1| | | | |296+0=296| | | ttttcaatagaaaagtcaaataatctaagtgtcaatcagtggatgattagataaaatatg atatatgtaaatcatggaatactatgcagccagtatggtatgaattcagtgtgaccagcc cctggacaagggcttgagtggatgggatggatcatcacctacactgggaacccaacatat accaacggcttcacaggacggtttctattctccatggacacctctgtcagcatggcgtat ctgcagatcagcagcctaaaggctgaggacacggccgtgtatgactgtatgagaga
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Mikaël Salson authored
Maybe we don't need to monitor default behaviour changes in every test. So I set the seed as a parameter to avoid test failures.
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Mikaël Salson authored
For IGH default seed changed (from #####-##### to ######-######) which changes segmentation results (and improves them!). Should we provide the seed to be used as a parameter to avoid such changes? Or should we let the test as it is to monitor changes in default behaviour?
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Marc Duez authored
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Mathieu Giraud authored
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Mathieu Giraud authored
We have already MAX_CLONES limiting the default output. In a typical MRD setup, the previous value of 0.1 was not meaningful.
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
In fact, it could be faster to use MapKmer for very short sets of reads... but Vidjil focuses on HTS datasets.
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Marc Duez authored
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Marc Duez authored
- give an html box for the star icon (needed for watir test)
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Marc Duez authored
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- 24 Mar, 2014 2 commits