Home
last modified time | relevance | path

Searched refs:query_gap (Results 1 – 9 of 9) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/
H A Dhspfilter_mapper.c380 Int4 query_gap = 0; in s_ComputeAlignmentScore() local
393 query_gap++; in s_ComputeAlignmentScore()
428 if (query_gap > 0) { in s_ComputeAlignmentScore()
430 query_gap = 0; in s_ComputeAlignmentScore()
538 Int4 query_gap = in s_ComputeChainScore() local
1490 Int4 query_gap; in s_MergeHSPs() local
1569 if (query_gap > 0) { in s_MergeHSPs()
1574 query_gap; in s_MergeHSPs()
1580 query_gap; in s_MergeHSPs()
1667 if (query_gap > 0) { in s_MergeHSPs()
[all …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/
H A Dhspfilter_mapper.c380 Int4 query_gap = 0; in s_ComputeAlignmentScore() local
393 query_gap++; in s_ComputeAlignmentScore()
428 if (query_gap > 0) { in s_ComputeAlignmentScore()
430 query_gap = 0; in s_ComputeAlignmentScore()
538 Int4 query_gap = in s_ComputeChainScore() local
1490 Int4 query_gap; in s_MergeHSPs() local
1569 if (query_gap > 0) { in s_MergeHSPs()
1574 query_gap; in s_MergeHSPs()
1580 query_gap; in s_MergeHSPs()
1667 if (query_gap > 0) { in s_MergeHSPs()
[all …]
/dports/biology/gmap/gmap-2020-09-12/src/
H A Dsimplepair.c531 int query_gap; in compute_cigar_standard() local
674 query_gap = this->querypos - exon_queryend; in compute_cigar_standard()
675 assert(query_gap >= 0); in compute_cigar_standard()
676 if (query_gap > 0) { in compute_cigar_standard()
683 sprintf(token,"%uI",query_gap); in compute_cigar_standard()
812 int query_gap; in compute_cigar_extended() local
958 query_gap = this->querypos - exon_queryend; in compute_cigar_extended()
959 assert(query_gap >= 0); in compute_cigar_extended()
960 if (query_gap > 0) { in compute_cigar_extended()
967 sprintf(token,"%uI",query_gap); in compute_cigar_extended()
H A Dpair.c5237 int query_gap; in compute_cigar_standard() local
5381 assert(query_gap >= 0); in compute_cigar_standard()
5382 if (query_gap > 0) { in compute_cigar_standard()
5389 sprintf(token,"%uI",query_gap); in compute_cigar_standard()
5518 int query_gap; in compute_cigar_extended() local
5665 assert(query_gap >= 0); in compute_cigar_extended()
5666 if (query_gap > 0) { in compute_cigar_extended()
5673 sprintf(token,"%uI",query_gap); in compute_cigar_extended()
6449 int query_gap;
6628 assert(query_gap >= 0);
[all …]
H A Dstage3.c2753 query_gap = this->querypos - exon_queryend; in fix_adjacent_indels()
2754 if (query_gap > 0) { in fix_adjacent_indels()
2756 debug4(printf("%dI",query_gap)); in fix_adjacent_indels()
2758 last_token_length = query_gap; in fix_adjacent_indels()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dmagicblast.cpp237 int query_gap = hsp->query.offset - prev->query.end; in s_ComputeBtopAndIdentity() local
238 if (query_gap > 0) { in s_ComputeBtopAndIdentity()
239 btop += (string)"_" + NStr::IntToString(query_gap) + "_"; in s_ComputeBtopAndIdentity()
242 else if (query_gap < 0) { in s_ComputeBtopAndIdentity()
243 btop += (string)"(" + NStr::IntToString(-query_gap) + ")"; in s_ComputeBtopAndIdentity()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dmagicblast.cpp237 int query_gap = hsp->query.offset - prev->query.end; in s_ComputeBtopAndIdentity() local
238 if (query_gap > 0) { in s_ComputeBtopAndIdentity()
239 btop += (string)"_" + NStr::IntToString(query_gap) + "_"; in s_ComputeBtopAndIdentity()
242 else if (query_gap < 0) { in s_ComputeBtopAndIdentity()
243 btop += (string)"(" + NStr::IntToString(-query_gap) + ")"; in s_ComputeBtopAndIdentity()
/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dhspfilter_mapper.c1420 Int4 query_gap; in s_MergeHSPs() local
1439 if (query_gap < 0 || subject_gap < 0 || query_gap > 1 || in s_MergeHSPs()
1440 query_gap != subject_gap) { in s_MergeHSPs()
1446 MAX(query_gap, subject_gap); in s_MergeHSPs()
1473 if (query_gap == subject_gap) { in s_MergeHSPs()
1474 mismatches = query_gap; in s_MergeHSPs()
2665 ASSERT(query_ext_len <= query_gap); in s_ExtendAlignment()
2671 while (query_ext_len < query_gap) { in s_ExtendAlignment()
2775 Int4 query_gap; in s_FindSpliceJunctionsForGap() local
2853 query_gap - 2 - q; in s_FindSpliceJunctionsForGap()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/magicblast/
H A Dmagicblast_util.cpp1249 int query_gap = (*next_exon)->GetProduct_start().GetNucpos() - in PrintSAM() local
1251 if (query_gap > 0) { in PrintSAM()
1252 cigar += NStr::IntToString(query_gap); in PrintSAM()
1255 edit_distance += query_gap; in PrintSAM()