- 13 Jun, 2018 40 commits
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Cyprien Borée authored
For more informations see #3268
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Cyprien Borée authored
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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Cyprien Borée authored
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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Cyprien Borée authored
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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Cyprien Borée authored
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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Cyprien Borée authored
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Cyprien Borée authored
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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Cyprien Borée authored
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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Cyprien Borée authored
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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Cyprien Borée authored
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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Cyprien Borée authored
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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Cyprien Borée authored
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Cyprien Borée authored
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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Cyprien Borée authored
Since the new option -Z will be added, the case where all K-mers will be selected to filter will be represented by -Z -1. For more informations about it, see #3268 and #3264.
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Cyprien Borée authored
For the purpose of adding the -Z option (described in #3264), the -H option will show its description.
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Mathieu Giraud authored
Incidentally close #3271.
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Cyprien Borée authored
Sequences are equal before 110bp so the alternative is valid. For more informations see #3262
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Cyprien Borée authored
Since some sequences are identical, we can add them as a result for the test. For more informations about it, see #3223 and #3262.
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Cyprien Borée authored
Since some sequences are identical, we can add them as a result for the test. For more informations about it, see #3223 and #3262.
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Cyprien Borée authored
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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Cyprien Borée authored
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Cyprien Borée authored
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Cyprien Borée authored
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Cyprien Borée authored
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Cyprien Borée authored
For more informations see #3217
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Cyprien Borée authored
To get the genes with the same number of occurences (described in #3217 )
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Cyprien Borée authored
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Cyprien Borée authored
This test assure that when a sequence is used to filter a BioReader, we find the sequence back in the result when we provide '1' as the most significant K-mer. Also it assures that the final BioReader has a size less than the original one. For more informations see #3217
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Cyprien Borée authored
The gene counter was already at 1 when doing the first loop since the previousKmerOccurs was initiated with '0'. To avoid that, it's now initiate with the value of the first member of the set. Also a simple simplification for the gene counter (deleted the empty if and replaced it with the opposite condition) For more informations #see 3217
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Cyprien Borée authored
The comparator checks if the two KmerAffect have the same number of occurences. If it is the case, then the Comparator use the comparison operators defined in the KmerAffect class to compare the KmerAffects. If the two KmerAffect doesn't have the same number of occurences, the Comparator returns true for the one that have the most of them. For more informations see #3217
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Cyprien Borée authored
If two K-mers occurs both the same amount of times, we want them both. Even if the number of significant K-mers is reached. For example if we want the 10 most significant K-mers but the 4th has two K-mers with the same value we take them both instead of one. For more informations, see #3217
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Cyprien Borée authored
The ascii shifting is no longer a requirement since the ascii value of a AMBIGUOUS and UNKNOWN Kmer are above 127 and thus, unreachable. For more informations see #3250
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Cyprien Borée authored
In buildAutomaton the seed parameter wasn't used since it was only provided through the insert method. It has been fixed. For more informations see #3217 and #3217 (comment 93122)
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Cyprien Borée authored
To avoid dealing with the ascii n°94 and n°63 (for the ambiguous and unknown) the strand changed (so the ascii value is above 127) For more informations see #3250
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Cyprien Borée authored
The toString method in KmerAffect was not using the already created methods toStringSigns and toStringValue.
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Cyprien Borée authored
Before, when the filtered bioreader contained less than 2 sequences the original bioreader was returned, it's no longer the case. See #3239 to know why.
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Mikaël Salson authored
See #3238.
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Cyprien Borée authored
(squashed from earlier commits)
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Cyprien Borée authored
See #920 and #3190. (squashed from earlier commits)
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Cyprien Borée authored
See #920 and #3191. (squashed from earlier commits)
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