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Searched refs:query_begin (Results 1 – 25 of 40) sorted by relevance

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/dports/biology/diamond/diamond-2.0.13/src/output/daa/
H A Ddaa_record.cpp63 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 >>()
/dports/biology/seqan1/seqan-1.3.1/seqan/blast/
H A Dblast_hsp.h106 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 …]
/dports/biology/vcflib/vcflib-1.0.2/src/
H A Dssw_cpp.cpp66 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()
H A Dssw_cpp.hpp26 int32_t query_begin; // Query begin position of the best alignment member
39 query_begin = 0; in Clear()
/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/
H A Dssw_cpp.cpp57 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()
H A Dssw_cpp.hpp17 int32_t query_begin; // Query begin position of the best alignment member
30 query_begin = 0; in Clear()
/dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/src/
H A Dssw_cpp.cpp57 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()
/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/
H A Dssw_cpp.cpp57 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()
H A Dssw_cpp.hpp17 int32_t query_begin; // Query begin position of the best alignment member
30 query_begin = 0; in Clear()
/dports/net/lft/lft-3.91/
H A Dwhois.c1051 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 …]
/dports/biology/diamond/diamond-2.0.13/src/output/
H A Doutput_format.cpp54 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()
/dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/SeqLib/
H A Dssw_cpp.h15 int32_t query_begin; // Query begin position of the best alignment member
28 query_begin = 0; in Clear()
/dports/biology/diamond/diamond-2.0.13/src/basic/
H A Dhssp.cpp277 …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()
/dports/www/qt5-webengine/qtwebengine-everywhere-src-5.15.2/src/3rdparty/chromium/url/android/
H A Dparsed_android.cc64 jint query_begin, in JNI_Parsed_CreateNative() argument
83 parsed->query.begin = query_begin; in JNI_Parsed_CreateNative()
/dports/www/chromium-legacy/chromium-88.0.4324.182/url/android/
H A Dparsed_android.cc64 jint query_begin, in JNI_Parsed_CreateNative() argument
83 parsed->query.begin = query_begin; in JNI_Parsed_CreateNative()
/dports/devel/grpc130/grpc-1.30.2/src/core/lib/uri/
H A Duri_parser.cc196 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()
/dports/devel/grpc134/grpc-1.34.1/src/core/lib/uri/
H A Duri_parser.cc190 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()
/dports/www/chromium-legacy/chromium-88.0.4324.182/third_party/grpc/src/src/core/lib/uri/
H A Duri_parser.cc196 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()
/dports/biology/seqan1/seqan-1.3.1/seqan/misc/
H A Dmisc_interval_tree.h1584 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);
/dports/devel/cpprestsdk/cpprestsdk-2.10.16/Release/src/uri/
H A Duri.cpp160 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/misc/
H A Dinterval_tree.h1510 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);
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/misc/
H A Dinterval_tree.h1510 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);
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/misc/
H A Dinterval_tree.h1525 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);
/dports/biology/diamond/diamond-2.0.13/src/search/
H A Dstage2.cpp143 uint32_t query_begin, in search_tile() argument
151 const SeedLoc* q_begin = q + query_begin, *s_begin = s + subject_begin; in search_tile()
/dports/math/moab/fathomteam-moab-7bde9dfb84a8/src/
H A DWriteUtil.hpp298 get_entity_list_pointers(Range::const_iterator query_begin,

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