| /dports/biology/bowtie/bowtie-1.3.1/ |
| H A D | ebwt_search_util.h | 69 bool repOk(uint32_t qualMax, uint32_t slen, const BTString& quals, bool maqPenalty) { in repOk() argument
74 qual += mmPenalty(maqPenalty, phredCharToPhredQual(quals[entry.pos0])); in repOk()
78 qual += mmPenalty(maqPenalty, phredCharToPhredQual(quals[entry.pos1])); in repOk()
82 qual += mmPenalty(maqPenalty, phredCharToPhredQual(quals[entry.pos2])); in repOk()
314 bool maqPenalty = true)
328 uint8_t oldQual0 = mmPenalty(maqPenalty, phredCharToPhredQual(quals[tpos0]));
339 uint8_t oldQual1 = mmPenalty(maqPenalty, phredCharToPhredQual(quals[tpos1]));
351 uint8_t oldQual2 = mmPenalty(maqPenalty, phredCharToPhredQual(quals[tpos2]));
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| H A D | aligner_0mm.h | 39 bool maqPenalty, in UnpairedExactAlignerV1Factory() argument
56 maqPenalty_(maqPenalty), in UnpairedExactAlignerV1Factory()
166 bool maqPenalty, in PairedExactAlignerV1Factory() argument
193 maqPenalty_(maqPenalty), in PairedExactAlignerV1Factory()
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| H A D | aligner_1mm.h | 40 bool maqPenalty, in Unpaired1mmAlignerV1Factory() argument
58 maqPenalty_(maqPenalty), in Unpaired1mmAlignerV1Factory()
206 bool maqPenalty, in Paired1mmAlignerV1Factory() argument
234 maqPenalty_(maqPenalty), in Paired1mmAlignerV1Factory()
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| H A D | aligner_23mm.h | 40 bool maqPenalty, in Unpaired23mmAlignerV1Factory() argument
59 maqPenalty_(maqPenalty), in Unpaired23mmAlignerV1Factory()
278 bool maqPenalty, in Paired23mmAlignerV1Factory()
307 maqPenalty_(maqPenalty), in Paired23mmAlignerV1Factory()
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| H A D | ebwt_search_backtrack.h | 42 bool maqPenalty = true) :
53 _maqPenalty(maqPenalty), in _qry()
1800 bool maqPenalty,
1814 maqPenalty_(maqPenalty), in RangeSource()
2615 bool maqPenalty,
2626 maqPenalty_(maqPenalty), in ebwt_()
2679 bool maqPenalty, in EbwtRangeSourceDriver() argument
2699 maqPenalty_(maqPenalty), in EbwtRangeSourceDriver()
2853 bool maqPenalty,
2873 maqPenalty_(maqPenalty), in params_()
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| H A D | ref_aligner.h | 43 bool maqPenalty = false) :
45 qualMax_(qualMax), maqPenalty_(maqPenalty), refbuf_(buf_), in verbose_()
1929 Seed0RefAligner(bool verbose, bool quiet, uint32_t seedLen, uint32_t qualMax, bool maqPenalty) : in Seed0RefAligner() argument
1930 RefAligner(verbose, quiet, seedLen, qualMax, maqPenalty) { } in Seed0RefAligner()
2529 … Seed1RefAligner(bool verbose, bool quiet, uint32_t seedLen, uint32_t qualMax, bool maqPenalty) : in Seed1RefAligner() argument
2530 RefAligner(verbose, quiet, seedLen, qualMax, maqPenalty) { } in Seed1RefAligner()
3265 … Seed2RefAligner(bool verbose, bool quiet, uint32_t seedLen, uint32_t qualMax, bool maqPenalty) : in Seed2RefAligner() argument
3266 RefAligner(verbose, quiet, seedLen, qualMax, maqPenalty) { } in Seed2RefAligner()
4122 … Seed3RefAligner(bool verbose, bool quiet, uint32_t seedLen, uint32_t qualMax, bool maqPenalty) : in Seed3RefAligner() argument
4123 RefAligner(verbose, quiet, seedLen, qualMax, maqPenalty) { } in Seed3RefAligner()
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| H A D | aligner_seed_mm.h | 44 bool maqPenalty, in UnpairedSeedAlignerFactory() argument
67 maqPenalty_(maqPenalty), in UnpairedSeedAlignerFactory()
604 bool maqPenalty, in PairedSeedAlignerFactory()
636 maqPenalty_(maqPenalty), in PairedSeedAlignerFactory()
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