- 14 Jun, 2018 4 commits
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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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Mikaël Salson authored
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Mikaël Salson authored
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- 13 Jun, 2018 36 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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For more informations see #3217
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To get the genes with the same number of occurences (described in #3217 )
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