/dports/biology/hisat2/hisat2-2.2.1/ |
H A D | unique.h | 58 bool mate1, in bestIsUnique() argument 80 bool mate1, 114 bool mate1, in mapq() argument 135 assert_geq(s.best(mate1).score(), s.secbest(mate1).score()); in mapq() 136 size_t diff = s.best(mate1).score() - s.secbest(mate1).score(); in mapq() 189 bool mate1, in mapq() argument 198 VALID_AL_SCORE(s.secbest(mate1)); in mapq() 207 assert_geq(s.best(mate1), s.secbest(mate1)); in mapq() 208 equalSecbest = s.best(mate1) == s.secbest(mate1); in mapq() 215 !s.exhausted(mate1) && in mapq() [all …]
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H A D | hisat2 | 601 my $mate1 = (($fl & 64) != 0); 603 my $unp = !$mate1 && !$mate2; 621 if($conc && $mate1) { 625 } elsif(!$conc && $mate1) { 630 if($conc_disc && $mate1) {
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H A D | aligner_result.h | 2255 AlnScore best(bool mate1) const { return mate1 ? best1_ : best2_; } in best() argument 2257 bool exhausted(bool mate1) const { in exhausted() argument 2258 return mate1 ? exhausted1_ : exhausted2_; in exhausted() 2268 AlnScore secbestMate(bool mate1) const { in secbestMate() argument 2269 return mate1 ? secbest1_ : secbest2_; in secbestMate() 2279 AlnScore secbest(bool mate1) const { in secbest() argument 2281 if(mate1) { in secbest() 2292 return mate1 ? secbest1_ : secbest2_; in secbest()
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H A D | hisat_bp.cpp | 2683 bool mate1, in printMmsSkipMsg() argument 2688 os << "Warning: skipping mate #" << (mate1 ? '1' : '2') in printMmsSkipMsg() 2689 << " of read '" << (mate1 ? ps.bufa().name : ps.bufb().name) in printMmsSkipMsg() 2703 bool mate1) in printLenSkipMsg() argument 2707 os << "Warning: skipping mate #" << (mate1 ? '1' : '2') in printLenSkipMsg() 2708 << " of read '" << (mate1 ? ps.bufa().name : ps.bufb().name) in printLenSkipMsg() 2720 bool mate1) in printLocalScoreMsg() argument 2725 << "--local mode for mate #" << (mate1 ? '1' : '2') in printLocalScoreMsg() 2726 << " of read '" << (mate1 ? ps.bufa().name : ps.bufb().name) in printLocalScoreMsg() 2739 bool mate1) in printEEScoreMsg() argument [all …]
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H A D | hisat2.cpp | 3017 bool mate1, in printMmsSkipMsg() argument 3022 os << "Warning: skipping mate #" << (mate1 ? '1' : '2') in printMmsSkipMsg() 3023 << " of read '" << (mate1 ? ps.bufa().name : ps.bufb().name) in printMmsSkipMsg() 3037 bool mate1) in printLenSkipMsg() argument 3041 os << "Warning: skipping mate #" << (mate1 ? '1' : '2') in printLenSkipMsg() 3042 << " of read '" << (mate1 ? ps.bufa().name : ps.bufb().name) in printLenSkipMsg() 3054 bool mate1) in printLocalScoreMsg() argument 3059 << "--local mode for mate #" << (mate1 ? '1' : '2') in printLocalScoreMsg() 3060 << " of read '" << (mate1 ? ps.bufa().name : ps.bufb().name) in printLocalScoreMsg() 3073 bool mate1) in printEEScoreMsg() argument [all …]
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H A D | aln_sink.h | 460 bool foundUnpaired(bool mate1, bool repeat = false); 522 inline bool doneUnpaired(bool mate1) const { in doneUnpaired() argument 523 return mate1 ? doneUnpair1_ : doneUnpair2_; in doneUnpaired() 531 inline bool doneWithMate(bool mate1) const { in doneWithMate() argument 532 bool doneUnpair = mate1 ? doneUnpair1_ : doneUnpair2_; in doneWithMate() 533 uint64_t nun = mate1 ? nunpair1_ : nunpair2_; in doneWithMate()
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H A D | aln_sink.cpp | 117 bool ReportingState::foundUnpaired(bool mate1, bool repeat) { in foundUnpaired() argument 121 if(mate1) { in foundUnpaired()
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/dports/biology/bowtie/bowtie-1.3.1/ |
H A D | aligner_seed_mm.h | 90 bool mate1 = true; in create() local 121 bool mate1 = true; in create() local 216 bool mate1 = true; in create() local 329 bool mate1 = true; in create() local 708 bool mate1 = true; in create() local 725 bool mate1 = false; in create() local 742 bool mate1 = true; in create() local 778 bool mate1 = true; in create() local 866 bool mate1 = true; in create() local 956 bool mate1 = true; in create() local [all …]
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H A D | range.h | 20 fw(true), mate1(true), ebwt(NULL) in Range() 40 bool mate1; // read aligned is #1 mate/single? member
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H A D | aligner.h | 1065 r.mate1 = !off1; in resolveOutstandingInRef() 1691 r.mate1 ? qlen1_ : qlen2_, in advance() 1798 assert(!(r.mate1 ? doneSe1_ : doneSe2_)); in reportSe() 1800 Read* buf = r.mate1 ? bufa_ : bufb_; in reportSe() 1802 uint32_t len = r.mate1 ? alen_ : blen_; in reportSe() 1828 if(r.mate1) doneSe1_ = true; in reportSe() 1884 bool matchRight = (pairFw ? range.mate1 : !range.mate1); in resolveOutstandingInRef() 1890 fw ? (range.mate1 ? patsrc_->bufb().patFw : in resolveOutstandingInRef() 1896 fw ? (range.mate1 ? patsrc_->bufb().qual : in resolveOutstandingInRef() 1898 (range.mate1 ? patsrc_->bufb().qualRev : in resolveOutstandingInRef() [all …]
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H A D | range_source.h | 1672 virtual bool mate1() const = 0; 1728 bool mate1, in SingleRangeSourceDriver() argument 1733 len_(0), mate1_(mate1), in SingleRangeSourceDriver() 1845 rs_->range().mate1 = mate1_; in range() 1853 bool mate1() const { in mate1() function 1919 virtual bool mate1() const { in mate1() function 2003 virtual bool mate1() const { in mate1() function 2004 return rss_[0]->mate1(); in mate1() 2222 virtual bool mate1() const { in mate1() function 2223 return rss_[0]->mate1(); in mate1() [all …]
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H A D | ebwt_search_backtrack.h | 2692 bool mate1, in EbwtRangeSourceDriver() argument 2697 quiet, mate1, 0, pool, btCnt), in EbwtRangeSourceDriver() 2866 bool mate1, 2886 mate1_(mate1), in params_() 2946 bool mate1) : in EbwtSeededRangeSourceDriver() argument 2950 mate1_(mate1), seedRange_(0) in EbwtSeededRangeSourceDriver() 3111 r.mate1 = mate1_; in range() 3119 virtual bool mate1() const { in mate1() function
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/dports/biology/bowtie2/bowtie2-2.4.4/ |
H A D | unique.h | 59 bool mate1, in bestIsUnique() argument 65 return !VALID_AL_SCORE(s.bestUnchosenScore(mate1)); in bestIsUnique() 81 bool mate1, 115 bool mate1, in mapq() argument 136 assert_geq(s.bestScore(mate1).score(), s.bestUnchosenScore(mate1).score()); in mapq() 137 size_t diff = s.bestScore(mate1).score() - s.bestUnchosenScore(mate1).score(); in mapq() 190 bool mate1, in mapq() argument 199 VALID_AL_SCORE(s.bestUnchosenScore(mate1)); in mapq() 436 bool mate1, in mapq() argument 453 TAlScore best = s.bestScore(mate1).score(); in mapq() [all …]
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H A D | aligner_result.h | 1853 AlnScore bestUnchosenPScore(bool mate1) const { in bestUnchosenPScore() argument 1854 return mate1 ? bestUnchosenP1Score_ : bestUnchosenP2Score_; in bestUnchosenPScore() 1860 AlnScore bestUnchosenPDist(bool mate1) const { in bestUnchosenPDist() argument 1861 return mate1 ? bestUnchosenP1Dist_ : bestUnchosenP2Dist_; in bestUnchosenPDist() 1868 AlnScore bestUnchosenScore(bool mate1) const { in bestUnchosenScore() argument 1876 AlnScore bestUnchosenDist(bool mate1) const { in bestUnchosenDist() argument 1880 bool exhausted(bool mate1) const { in exhausted() argument 1881 return mate1 ? exhausted1_ : exhausted2_; in exhausted() 1888 AlnScore bestScore(bool mate1) const { in bestScore() argument 1896 AlnScore bestDist(bool mate1) const { in bestDist() argument [all …]
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H A D | bowtie2 | 582 my $mate1 = (($fl & 64) != 0); 584 my $unp = !$mate1 && !$mate2; 601 if ($conc && $mate1) { 605 } elsif(!$conc && $mate1) { 613 if ($mate1) {
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H A D | aln_sink.h | 400 bool foundUnpaired(bool mate1); 460 inline bool doneUnpaired(bool mate1) const { in doneUnpaired() argument 461 return mate1 ? doneUnpair1_ : doneUnpair2_; in doneUnpaired() 469 inline bool doneWithMate(bool mate1) const { in doneWithMate() argument 470 bool doneUnpair = mate1 ? doneUnpair1_ : doneUnpair2_; in doneWithMate() 471 uint64_t nun = mate1 ? nunpair1_ : nunpair2_; in doneWithMate()
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H A D | sam.cpp | 547 bool mate1 = rd.mate < 2; // first iteration: self in printAlignedOptFlags() local 548 if(self > 0) mate1 = !mate1; // second iteration: opposite in printAlignedOptFlags() 550 sco = summ.bestUnchosenPScore(mate1); in printAlignedOptFlags() 559 thirdBest[self] = mate1 ? prm.bestLtMinscMate1 : prm.bestLtMinscMate2; in printAlignedOptFlags() 562 if(summ.bestUnchosenPDist(mate1).valid()) { in printAlignedOptFlags() 563 diffEd[self] = best[self].basesAligned() - summ.bestUnchosenPDist(mate1).basesAligned(); in printAlignedOptFlags()
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H A D | bt2_search.cpp | 2761 bool mate1, in printMmsSkipMsg() argument 2766 os << "Warning: skipping mate #" << (mate1 ? '1' : '2') in printMmsSkipMsg() 2767 << " of read '" << (mate1 ? ps.read_a().name : ps.read_b().name) in printMmsSkipMsg() 2781 bool mate1) in printLenSkipMsg() argument 2785 os << "Warning: skipping mate #" << (mate1 ? '1' : '2') in printLenSkipMsg() 2786 << " of read '" << (mate1 ? ps.read_a().name : ps.read_b().name) in printLenSkipMsg() 2798 bool mate1) in printLocalScoreMsg() argument 2803 << "--local mode for mate #" << (mate1 ? '1' : '2') in printLocalScoreMsg() 2804 << " of read '" << (mate1 ? ps.read_a().name : ps.read_b().name) in printLocalScoreMsg() 2817 bool mate1) in printEEScoreMsg() argument [all …]
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/dports/devel/boost-docs/boost_1_72_0/libs/graph/example/ |
H A D | weighted_matching_example.cpp | 76 std::vector<graph_traits<my_graph>::vertex_descriptor> mate1(n_vertices), mate2(n_vertices); in main() local 77 maximum_weighted_matching(g, &mate1[0]); in main() 80 …< "Matching size is " << matching_size(g, &mate1[0]) << ", total weight is " << matching_weight_su… in main() 85 if (mate1[*vi] != graph_traits<my_graph>::null_vertex() && *vi < mate1[*vi]) in main() 86 std::cout << "{" << *vi << ", " << mate1[*vi] << "}" << std::endl; in main() 105 assert(matching_weight_sum(g, &mate1[0]) == matching_weight_sum(g, &mate2[0])); in main()
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/dports/devel/boost-python-libs/boost_1_72_0/libs/graph/example/ |
H A D | weighted_matching_example.cpp | 76 std::vector<graph_traits<my_graph>::vertex_descriptor> mate1(n_vertices), mate2(n_vertices); in main() local 77 maximum_weighted_matching(g, &mate1[0]); in main() 80 …< "Matching size is " << matching_size(g, &mate1[0]) << ", total weight is " << matching_weight_su… in main() 85 if (mate1[*vi] != graph_traits<my_graph>::null_vertex() && *vi < mate1[*vi]) in main() 86 std::cout << "{" << *vi << ", " << mate1[*vi] << "}" << std::endl; in main() 105 assert(matching_weight_sum(g, &mate1[0]) == matching_weight_sum(g, &mate2[0])); in main()
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/dports/devel/boost-libs/boost_1_72_0/libs/graph/example/ |
H A D | weighted_matching_example.cpp | 76 std::vector<graph_traits<my_graph>::vertex_descriptor> mate1(n_vertices), mate2(n_vertices); in main() local 77 maximum_weighted_matching(g, &mate1[0]); in main() 80 …< "Matching size is " << matching_size(g, &mate1[0]) << ", total weight is " << matching_weight_su… in main() 85 if (mate1[*vi] != graph_traits<my_graph>::null_vertex() && *vi < mate1[*vi]) in main() 86 std::cout << "{" << *vi << ", " << mate1[*vi] << "}" << std::endl; in main() 105 assert(matching_weight_sum(g, &mate1[0]) == matching_weight_sum(g, &mate2[0])); in main()
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/dports/devel/hyperscan/boost_1_75_0/libs/graph/example/ |
H A D | weighted_matching_example.cpp | 79 std::vector< graph_traits< my_graph >::vertex_descriptor > mate1( in main() local 82 maximum_weighted_matching(g, &mate1[0]); in main() 85 std::cout << "Matching size is " << matching_size(g, &mate1[0]) in main() 86 << ", total weight is " << matching_weight_sum(g, &mate1[0]) in main() 92 if (mate1[*vi] != graph_traits< my_graph >::null_vertex() in main() 93 && *vi < mate1[*vi]) in main() 94 std::cout << "{" << *vi << ", " << mate1[*vi] << "}" << std::endl; in main() 118 matching_weight_sum(g, &mate1[0]) == matching_weight_sum(g, &mate2[0])); in main()
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/dports/biology/bowtie/bowtie-1.3.1/scripts/test/ |
H A D | random_bowtie_tests.pl | 855 my $m = substr($mate1, index($mate1, "/")+1); 873 my $m = substr($mate1, index($mate1, "/")+1); 882 if($mate1 ne $lastread && !$pe) { 883 die "Read $mate1 appears multiple times non-consecutively" if defined($readcount{$mate1}); 886 !defined($readStratum{$mate1}) || 889 $readStratum{$mate1} = $stratum1; 894 my $tmp = $mate1; $mate1 = $mate2; $mate2 = $tmp; 906 $readStratum1{$mate1} = $stratum1; 909 $lastread = $mate1; 910 $readcount{$mate1}++; [all …]
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/dports/biology/bowtie/bowtie-1.3.1/scripts/ |
H A D | fastq_to_tabbed.pl | 43 my $mate1 = ""; 48 "1=s" => \$mate1, 71 my @mate1s = split(/,/, $mate1);
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H A D | pe_verify.pl | 142 my $mate1 = ($l1rs[$#l1rs] eq "1"); 143 my $mate1str = $mate1 ? "1" : "0"; 169 if($mate1) { $pesFw++; } else { $pesRc++; }
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