Searched refs:penMmcMin (Results 1 – 8 of 8) sorted by relevance
| /dports/biology/bowtie2/bowtie2-2.4.4/ |
| H A D | aligner_seed_policy.cpp | 256 int& penMmcMin, in parseString() argument
278 penMmcMin = DEFAULT_MM_PENALTY_MIN; in parseString()
386 penMmcMin = penMmcMax; in parseString()
400 tmpss >> penMmcMin; in parseString()
402 penMmcMin = DEFAULT_MM_PENALTY_MIN; in parseString()
404 if(penMmcMin > penMmcMax) { in parseString()
406 << ") is less than minimum penalty (" << penMmcMin in parseString()
422 penMmcMin = penMmcMax; in parseString()
702 assert_eq(DEFAULT_MM_PENALTY_MIN, penMmcMin); in main()
808 assert_eq(DEFAULT_MM_PENALTY_MIN, penMmcMin); in main()
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| H A D | bt2_dp.cpp | 44 static int penMmcMin; // min mm penalty variable
78 penMmcMin = DEFAULT_MM_PENALTY_MIN; in resetOptions()
353 penMmcMin = penMmcMax; in parseOption()
367 tmpss >> penMmcMin; in parseOption()
369 penMmcMin = DEFAULT_MM_PENALTY_MIN; in parseOption()
371 if(penMmcMin > penMmcMax) { in parseOption()
373 << ") is less than minimum penalty (" << penMmcMin in parseOption()
692 penMmcMin, // min mm pelanty in main()
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| H A D | aligner_seed_policy.h | 214 int& penMmcMin,
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| H A D | bt2_search.cpp | 197 static int penMmcMin; // min mm penalty variable
398 penMmcMin = DEFAULT_MM_PENALTY_MIN; in resetOptions()
1654 penMmcMin, in parseOptions()
4900 penMmcMin, // min mm pelanty in driver()
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| /dports/biology/hisat2/hisat2-2.2.1/ |
| H A D | aligner_seed_policy.cpp | 256 int& penMmcMin, in parseString() argument
282 penMmcMin = DEFAULT_MM_PENALTY_MIN; in parseString()
393 penMmcMin = penMmcMax; in parseString()
407 tmpss >> penMmcMin; in parseString()
409 penMmcMin = DEFAULT_MM_PENALTY_MIN; in parseString()
411 if(penMmcMin > penMmcMax) { in parseString()
413 << ") is less than minimum penalty (" << penMmcMin in parseString()
729 assert_eq(DEFAULT_MM_PENALTY_MIN, penMmcMin); in main()
838 assert_eq(DEFAULT_MM_PENALTY_MIN, penMmcMin); in main()
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| H A D | aligner_seed_policy.h | 213 int& penMmcMin,
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| H A D | hisat_bp.cpp | 186 static int penMmcMin; // min mm penalty variable
385 penMmcMin = DEFAULT_MM_PENALTY_MIN; in resetOptions()
1549 penMmcMin, in parseOptions()
3541 penMmcMin, // min mm pelanty in driver()
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| H A D | hisat2.cpp | 188 static int penMmcMin; // min mm penalty variable
429 penMmcMin = DEFAULT_MM_PENALTY_MIN; in resetOptions()
1855 penMmcMin, in parseOptions()
3924 penMmcMin, // min mm penalty in driver()
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