Searched refs:rflank (Results 1 – 9 of 9) sorted by relevance
| /dports/biology/vt/vt-0.57721/ |
| H A D | set_ref.cpp | 217 char* rflank = 0; in set_ref() local
220 … if (end1<region1[1]) rflank = rs->fetch_seq(bcf_get_chrom(h,v), end1+1, region1[1]); in set_ref()
240 if (rflank) std::cerr << "rflank: " << rflank << "\n"; in set_ref()
248 if (rflank) kputs(rflank, &new_alleles); in set_ref()
252 if (rflank) free(rflank); in set_ref()
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| H A D | align.cpp | 64 std::string rflank; member in __anonf1c5588d0111::Igor
124 rflank = arg_rflank.getValue(); in Igor()
172 if (rflank=="") in align()
184 hmm.set_model(lflank.c_str(), ru.c_str(), rflank.c_str()); in align()
238 if (rflank=="") in align()
261 hmm.set_model(ru.c_str(), rflank.c_str()); in align()
275 if (rflank=="") in align()
298 hmm.set_model(ru.c_str(), rflank.c_str()); in align()
406 std::clog << " [r] rflank " << rflank << "\n"; in print_options()
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| H A D | flank_detector.cpp | 190 std::string rflank; in detect_flanks() local
202 rs->fetch_seq(variant.chrom, vntr.exact_end1+1, vntr.exact_end1+5, rflank); in detect_flanks()
205 seq.append(rflank); in detect_flanks()
207 rfhmm->set_model(vntr.fuzzy_ru.c_str(), rflank.c_str()); in detect_flanks()
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| H A D | vntr.h | 73 …std::string rflank; //right flank … variable
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| H A D | vntr.cpp | 45 rflank.clear(); in clear()
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| H A D | rfhmm.cpp | 307 void RFHMM::set_model(const char* motif, const char* rflank) in set_model() argument
314 model[RFLANK] = strdup(rflank); in set_model()
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| H A D | rfhmm_x.cpp | 307 void RFHMM_X::set_model(const char* motif, const char* rflank) in set_model() argument
314 model[RFLANK] = strdup(rflank); in set_model()
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| H A D | chmm.h | 184 void set_model(const char* lflank, const char* ru, const char* rflank);
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| H A D | chmm.cpp | 520 void CHMM::set_model(const char* lflank, const char* motif, const char* rflank) in set_model() argument
528 model[RFLANK] = strdup(rflank); in set_model()
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