/dports/biology/diamond/diamond-2.0.13/src/output/daa/ |
H A D | daa_record.cpp | 63 uint32_t query_begin, subject_begin; in operator >>() local 64 it.read_packed((flag >> 2) & 3, query_begin); in operator >>() 71 …r.frame = (flag&(1 << 6)) == 0 ? query_begin % 3 : 3 + (r.parent_.source_seq.size() - 1 - query_be… in operator >>() 72 r.set_translated_query_begin(query_begin, (unsigned)r.parent_.source_seq.size()); in operator >>() 76 r.query_range.begin_ = query_begin; in operator >>()
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/dports/biology/seqan1/seqan-1.3.1/seqan/blast/ |
H A D | blast_hsp.h | 106 unsigned int query_begin; variable 140 query_begin = other.query_begin; in BlastHsp() 160 query_begin = other.query_begin; 292 hsp.query_begin = pint; in _parseBlastHsp() 390 unsigned int query_begin; variable 427 query_begin = other.query_begin; in BlastHsp() 449 query_begin = other.query_begin; 591 hsp.query_begin = pint; in _parseBlastHsp() 686 unsigned int query_begin; variable 705 query_begin = other.query_begin; in BlastHsp() [all …]
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/dports/biology/vcflib/vcflib-1.0.2/src/ |
H A D | ssw_cpp.cpp | 66 al->query_begin = s_al.read_begin1; in ConvertAlignment() 75 if (al->query_begin > 0) { in ConvertAlignment() 76 uint32_t cigar = to_cigar_int(al->query_begin, 'S'); in ConvertAlignment() 78 cigar_string << al->query_begin << 'S'; in ConvertAlignment() 139 query += al->query_begin; in CalculateNumberMismatch() 145 if (al->query_begin > 0) { in CalculateNumberMismatch() 146 uint32_t cigar = to_cigar_int(al->query_begin, 'S'); in CalculateNumberMismatch() 148 new_cigar_string << al->query_begin << 'S'; in CalculateNumberMismatch()
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H A D | ssw_cpp.hpp | 26 int32_t query_begin; // Query begin position of the best alignment member 39 query_begin = 0; in Clear()
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/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
H A D | ssw_cpp.cpp | 57 al->query_begin = s_al.read_begin1; in ConvertAlignment() 66 if (al->query_begin > 0) { in ConvertAlignment() 67 uint32_t cigar = to_cigar_int(al->query_begin, 'S'); in ConvertAlignment() 69 cigar_string << al->query_begin << 'S'; in ConvertAlignment() 130 query += al->query_begin; in CalculateNumberMismatch() 136 if (al->query_begin > 0) { in CalculateNumberMismatch() 137 uint32_t cigar = to_cigar_int(al->query_begin, 'S'); in CalculateNumberMismatch() 139 new_cigar_string << al->query_begin << 'S'; in CalculateNumberMismatch()
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H A D | ssw_cpp.hpp | 17 int32_t query_begin; // Query begin position of the best alignment member 30 query_begin = 0; in Clear()
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/dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/src/ |
H A D | ssw_cpp.cpp | 57 al->query_begin = s_al.read_begin1; in ConvertAlignment() 66 if (al->query_begin > 0) { in ConvertAlignment() 67 uint32_t cigar = to_cigar_int(al->query_begin, 'S'); in ConvertAlignment() 69 cigar_string << al->query_begin << 'S'; in ConvertAlignment() 130 query += al->query_begin; in CalculateNumberMismatch() 136 if (al->query_begin > 0) { in CalculateNumberMismatch() 137 uint32_t cigar = to_cigar_int(al->query_begin, 'S'); in CalculateNumberMismatch() 139 new_cigar_string << al->query_begin << 'S'; in CalculateNumberMismatch()
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/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
H A D | ssw_cpp.cpp | 57 al->query_begin = s_al.read_begin1; in ConvertAlignment() 66 if (al->query_begin > 0) { in ConvertAlignment() 67 uint32_t cigar = to_cigar_int(al->query_begin, 'S'); in ConvertAlignment() 69 cigar_string << al->query_begin << 'S'; in ConvertAlignment() 130 query += al->query_begin; in CalculateNumberMismatch() 136 if (al->query_begin > 0) { in CalculateNumberMismatch() 137 uint32_t cigar = to_cigar_int(al->query_begin, 'S'); in CalculateNumberMismatch() 139 new_cigar_string << al->query_begin << 'S'; in CalculateNumberMismatch()
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H A D | ssw_cpp.hpp | 17 int32_t query_begin; // Query begin position of the best alignment member 30 query_begin = 0; in Clear()
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/dports/net/lft/lft-3.91/ |
H A D | whois.c | 1051 strcat(whob_query,query_begin); in w_display_rvbyasn_pwhois() 1093 strcat(whob_query,query_begin); in w_display_rvbytransitasn_pwhois() 1135 strcat(whob_query,query_begin); in w_display_contactsbyasn_pwhois() 1177 strcat(whob_query,query_begin); in w_display_networksbyasn_pwhois() 1198 const char *query_begin = "routeview prefix="; in w_display_rvbyprefix_pwhois() local 1219 strcat(whob_query,query_begin); in w_display_rvbyprefix_pwhois() 1239 const char *query_begin = "begin\n"; in w_display_bulkfromfile_pwhois() local 1311 strcat(whob_query, query_begin); in w_display_bulkfromfile_pwhois() 1419 strcat(whob_query, query_begin); in w_display_bulkfromfile_riswhois() 1448 const char *query_begin = "begin\n"; in w_display_bulkfromfile_cymru() local [all …]
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/dports/biology/diamond/diamond-2.0.13/src/output/ |
H A D | output_format.cpp | 54 f.read_packed((flag >> 2) & 3, query_begin); in read() 73 if (query_begin < query_end) in absolute_query_range() 74 return interval(query_begin, query_end + 1); in absolute_query_range() 76 return interval(query_end, query_begin + 1); in absolute_query_range()
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/dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/SeqLib/ |
H A D | ssw_cpp.h | 15 int32_t query_begin; // Query begin position of the best alignment member 28 query_begin = 0; in Clear()
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/dports/biology/diamond/diamond-2.0.13/src/basic/ |
H A D | hssp.cpp | 277 …frame = (r.flag&(1 << 6)) == 0 ? r.query_begin % 3 : 3 + (query_source_len - 1 - r.query_begin) % … in Hsp() 278 set_translated_query_begin(r.query_begin, query_source_len); in Hsp() 282 query_range.begin_ = r.query_begin; in Hsp()
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/dports/www/qt5-webengine/qtwebengine-everywhere-src-5.15.2/src/3rdparty/chromium/url/android/ |
H A D | parsed_android.cc | 64 jint query_begin, in JNI_Parsed_CreateNative() argument 83 parsed->query.begin = query_begin; in JNI_Parsed_CreateNative()
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/dports/www/chromium-legacy/chromium-88.0.4324.182/url/android/ |
H A D | parsed_android.cc | 64 jint query_begin, in JNI_Parsed_CreateNative() argument 83 parsed->query.begin = query_begin; in JNI_Parsed_CreateNative()
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/dports/devel/grpc130/grpc-1.30.2/src/core/lib/uri/ |
H A D | uri_parser.cc | 196 size_t query_begin = NOT_SET; in grpc_uri_parse() local 255 query_begin = ++i; in grpc_uri_parse() 280 uri->query = decode_and_copy_component(uri_text, query_begin, query_end); in grpc_uri_parse()
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/dports/devel/grpc134/grpc-1.34.1/src/core/lib/uri/ |
H A D | uri_parser.cc | 190 size_t query_begin = NOT_SET; in grpc_uri_parse() local 250 query_begin = ++i; in grpc_uri_parse() 275 uri->query = decode_and_copy_component(uri_text, query_begin, query_end); in grpc_uri_parse()
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/dports/www/chromium-legacy/chromium-88.0.4324.182/third_party/grpc/src/src/core/lib/uri/ |
H A D | uri_parser.cc | 196 size_t query_begin = NOT_SET; in grpc_uri_parse() local 255 query_begin = ++i; in grpc_uri_parse() 280 uri->query = decode_and_copy_component(uri_text, query_begin, query_end); in grpc_uri_parse()
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/dports/biology/seqan1/seqan-1.3.1/seqan/misc/ |
H A D | misc_interval_tree.h | 1584 findIntervals(IntervalTree<TValue,TCargo> & tree, TValue query_begin, TValue query_end, String<TCar… 1588 findIntervals(tree.g,tree.pm,query_begin,query_end,result); 1596 findIntervals(TGraph & g, TPropertyMap & pm, TValue query_begin, TValue query_end, String<TCargo> &… 1608 findIntervals(g, pm, act_knot, query_begin, query_end, result); 1617 TValue query_begin, 1635 if(act_prop.center < query_begin) // query interval is to the right of node center 1638 while(i < length(act_prop.list2) && rightBoundary(value(act_prop.list2,i)) > query_begin) 1682 findIntervals(g,pm, next_knot, query_begin, query_end, result);
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/dports/devel/cpprestsdk/cpprestsdk-2.10.16/Release/src/uri/ |
H A D | uri.cpp | 160 const utility::char_t* query_begin = nullptr; member 301 query_begin = p; in parse_from() 374 if (query_begin) in write_to() 376 components.m_query.assign(query_begin, query_end); in write_to()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/misc/ |
H A D | interval_tree.h | 1510 TValue2 query_begin, 1513 findIntervals(result, tree.g, tree.pm, query_begin, query_end); 1522 TValue query_begin, 1532 findIntervals(result, g, pm, act_knot, query_begin, query_end); 1547 TValue query_begin, 1564 if (act_prop.center < query_begin) // query interval is to the right of node center 1567 while (i<length(act_prop.list2) && rightBoundary(value(act_prop.list2, i))> query_begin) 1615 findIntervals(result, g, pm, next_knot, query_begin, query_end);
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/misc/ |
H A D | interval_tree.h | 1510 TValue2 query_begin, 1513 findIntervals(result, tree.g, tree.pm, query_begin, query_end); 1522 TValue query_begin, 1532 findIntervals(result, g, pm, act_knot, query_begin, query_end); 1547 TValue query_begin, 1564 if (act_prop.center < query_begin) // query interval is to the right of node center 1567 while (i<length(act_prop.list2) && rightBoundary(value(act_prop.list2, i))> query_begin) 1615 findIntervals(result, g, pm, next_knot, query_begin, query_end);
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/misc/ |
H A D | interval_tree.h | 1525 TValue2 query_begin, 1528 findIntervals(result, tree.g, tree.pm, query_begin, query_end); 1537 TValue query_begin, 1547 findIntervals(result, g, pm, act_knot, query_begin, query_end); 1562 TValue query_begin, 1579 if (act_prop.center < query_begin) // query interval is to the right of node center 1582 while (i<length(act_prop.list2) && rightBoundary(value(act_prop.list2, i))> query_begin) 1630 findIntervals(result, g, pm, next_knot, query_begin, query_end);
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/dports/biology/diamond/diamond-2.0.13/src/search/ |
H A D | stage2.cpp | 143 uint32_t query_begin, in search_tile() argument 151 const SeedLoc* q_begin = q + query_begin, *s_begin = s + subject_begin; in search_tile()
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/dports/math/moab/fathomteam-moab-7bde9dfb84a8/src/ |
H A D | WriteUtil.hpp | 298 get_entity_list_pointers(Range::const_iterator query_begin,
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