- 15 Jun, 2018 6 commits
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Cyprien Borée authored
The second part of the test now verify that previous sequences are still in the filtered BioReader even though a new ex-aequo has been found. For more informations see #3284
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Cyprien Borée authored
This reverts commit 53b44e2c.
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Cyprien Borée authored
In the second part of the test, the program verify that previous filtered sequences are still in the BioReader when there is one more ex-aequo found. For more informations about it, see #3279.
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For more informations see issue #3279
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Since the last way to compare produced segfault (due to undefined behaviour of the advance method), to bypass this problem we just look at the previous of occurences to see if it's the same as the last -1. For more informations see #3279.
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In order to be sure that the filter function returns the accurates sequences, every sequences is checked and also the size of them.
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- 14 Jun, 2018 3 commits
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Mikaël Salson authored
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Mikaël Salson authored
This reverts commit 82c5ff15. Those files are not used anymore and were there for tests purposes. This commit should not have been merged.
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Mathieu Giraud authored
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- 13 Jun, 2018 31 commits
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Mathieu Giraud authored
This is not the optimal way. See #3285.
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Mathieu Giraud authored
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Mikaël Salson authored
optimize FineSegmenter, filtering BioReader with an Aho-Corasick automaton Closes #920 and #3271 See merge request !199
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Mikaël Salson authored
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Mikaël Salson authored
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Opens #3279.
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Since kmer_threshold parameter became a signed int, there's the possibility that this parameter is a negative number. If it's the case the entire original BioReader is returned.
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For more informations see #3268
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Since a new parameter has been added to filterBioReader (representing the filter specifity) it has to be transmitted when calling the function. Otherwise the filter will do the filter on "NO_LIMIT_VALUE". For more informations see #3268
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Since a new parameter has been added, even the germline constructor call in the test need to use it to use the automaton. For more informations see #3268.
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A boolean parameter has been added in the Germline constructors in order to check if the automaton needs to be constructed or not. For example with -Z all, the automaton is not constructed. For more informations see #3268
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The FineSegmenter constructor handles the filtering of the germline. By default the value is "NO_LIMIT_VALUE", which means the filtering isn't active. For more informations about it #3268.
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In #3268 we want to add a specific command-line option for the filtering. The -Z has only been declared in the getopt. The remaining task is to check if -Z still has NO_LIMIT_VALUE as an argument. If so the automaton is not built, otherwise the automaton is built and the argument is used to filter the BioReader.
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If the program is call with -Z 0, the filter function use every K-mer with at least one match. 0 is defined by the constand ALL_KMERS_VALUE in tools.h For more informations see #3276
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This constant is representing -Z 0 parameter. It's used when the filter function is called on every k-mer with at least one match. For more informations see #3276
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Since in the future there might be another automaton (automaton_3), the pair_automaton variable has been changed to automaton_5 in many files. see #3267 and #3267 (comment 96152)
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Since the kmer_threshold parameter became a signed integer, some comparison were producing sign warnings due to -Wsign-compare g++ compiler. For more informations see #3270
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Since the threshold parameter can be -1 the threshold parameter has been switched to a signed integer (the default int in C/C++). Also the use of NO_LIMIT_VALUE is used insted of -1. For more informations see #3270
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For the purpose of adding the -Z option (described in #3264), the -H option will show its description.
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Incidentally close #3271.
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Sequences are equal before 110bp so the alternative is valid. For more informations see #3262
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When there is no sequences found in the filtered BioReader it throws a segfault. For more informations about it, see #3223
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