- 08 Mar, 2019 2 commits
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Mathieu Giraud authored
Ensure tab after name See merge request !430
- 07 Mar, 2019 2 commits
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Mikaël Salson authored
On each line we should have a + or - when segmented or an exclamation mark when unsegmented. A tab should always exist at least between the sequence name and the VDJ designation.
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Mikaël Salson authored
This should ease parsing the output.
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- 06 Mar, 2019 14 commits
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Mathieu Giraud authored
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Mikaël Salson authored
-c designations Closes #3772 See merge request !429
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Mikaël Salson authored
Better CLI11 error messages, link to documentation See merge request !428
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
see also should#31
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Mathieu Giraud authored
Add display the error message improved in the previous commit. see #3775
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Mathieu Giraud authored
close #3772.
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Mathieu Giraud authored
define and use failure_message_doc(), taking inspiration from FailureMessage::simple() see #3775
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Mathieu Giraud authored
See #3772.
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Mathieu Giraud authored
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Mathieu Giraud authored
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Mathieu Giraud authored
See #3772.
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Mathieu Giraud authored
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- 05 Mar, 2019 18 commits
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Mikaël Salson authored
Feature cs/3722 browsers from env or file See merge request !423
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Mikaël Salson authored
This cannot be properly tested in test_segmenter_page_errors.rb as we don't have a menu there
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Mikaël Salson authored
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tests/launch_functional_tests: select browsers from environment variable or from 'tested-browser' file Partially revert 02ca0a24. We want both to agnostically use 'launch_functional_tests', but also to be able to follow in a versioned file the supported browsers.
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Mikaël Salson authored
Use a fixed version of web2py Closes #3605 See merge request !419
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Mathieu Giraud authored
Update e-value on SEG_METHOD_ONE with Aho Closes #3773 See merge request !426
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Mathieu Giraud authored
was done twice in 40aef950 and 556d8b0b, but git merge did not understood what we meant there ;-)
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Mathieu Giraud authored
see #3773
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Mathieu Giraud authored
Random read sample for representative Closes #3764 See merge request !422
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Mikaël Salson authored
The dataset was generated to have a minority of sequences with a TTT insertion which would make it the sequence of choice with the default ReadScore (based on length and quality). On the contrary with a random sampler we should not be impacted by this insertion as it happens in the minority of sequences. Here is the command that generated the dataset: for i in $(seq 1 3500); do if [ $((RANDOM%3)) -ne 0 ]; then echo ">seq$i"; echo ctacctactactgtgccttgtgggaggtgatagtagtgattggatcaag; else echo ">seq$i"; echo cTTTtacctactactgtgccttgtgggaggtgatagtagtgattggatcaag; fi; done > test-random-consensus.fa
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Mikaël Salson authored
A reference cannot be redefined in C++.
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see #3764.
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Mikaël Salson authored
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Mikaël Salson authored
This was put in two different places and could lead to inconsistencies. Now the reads are necessarily selected in the same way.
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Mikaël Salson authored
Random score on a read makes possible to have a random sample of reads to compute the representative. Thus the representative will be built on a really representative sample. Our attempts to have a good quality sample have failed so far. Thus we attempt this solution. Fix #3764
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Mikaël Salson authored
Aho by default Closes #3419 and #2556 See merge request !78
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- 04 Mar, 2019 4 commits
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Mikaël Salson authored
Exit → return See merge request !425
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Mikaël Salson authored
Executing valgrind can take more time, thus we need to increase the default timeout to make sure the program has time to properly execute.
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Mikaël Salson authored
See 1a7bb7f8 for reason why. Fix (in part?) #3771
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Mikaël Salson authored
Feature a/3729 clean memory Closes #3729 See merge request !412
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