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Searched refs:mate1 (Results 1 – 25 of 44) sorted by relevance

12

/dports/biology/hisat2/hisat2-2.2.1/
H A Dunique.h58 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()
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H A Dhisat2601 my $mate1 = (($fl & 64) != 0);
603 my $unp = !$mate1 && !$mate2;
621 if($conc && $mate1) {
625 } elsif(!$conc && $mate1) {
630 if($conc_disc && $mate1) {
H A Daligner_result.h2255 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()
H A Dhisat_bp.cpp2683 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
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H A Dhisat2.cpp3017 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
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H A Daln_sink.h460 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()
H A Daln_sink.cpp117 bool ReportingState::foundUnpaired(bool mate1, bool repeat) { in foundUnpaired() argument
121 if(mate1) { in foundUnpaired()
/dports/biology/bowtie/bowtie-1.3.1/
H A Daligner_seed_mm.h90 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
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H A Drange.h20 fw(true), mate1(true), ebwt(NULL) in Range()
40 bool mate1; // read aligned is #1 mate/single? member
H A Daligner.h1065 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()
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H A Drange_source.h1672 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()
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H A Debwt_search_backtrack.h2692 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
/dports/biology/bowtie2/bowtie2-2.4.4/
H A Dunique.h59 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()
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H A Daligner_result.h1853 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
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H A Dbowtie2582 my $mate1 = (($fl & 64) != 0);
584 my $unp = !$mate1 && !$mate2;
601 if ($conc && $mate1) {
605 } elsif(!$conc && $mate1) {
613 if ($mate1) {
H A Daln_sink.h400 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()
H A Dsam.cpp547 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()
H A Dbt2_search.cpp2761 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
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/dports/devel/boost-docs/boost_1_72_0/libs/graph/example/
H A Dweighted_matching_example.cpp76 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()
/dports/devel/boost-python-libs/boost_1_72_0/libs/graph/example/
H A Dweighted_matching_example.cpp76 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()
/dports/devel/boost-libs/boost_1_72_0/libs/graph/example/
H A Dweighted_matching_example.cpp76 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()
/dports/devel/hyperscan/boost_1_75_0/libs/graph/example/
H A Dweighted_matching_example.cpp79 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()
/dports/biology/bowtie/bowtie-1.3.1/scripts/test/
H A Drandom_bowtie_tests.pl855 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}++;
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/dports/biology/bowtie/bowtie-1.3.1/scripts/
H A Dfastq_to_tabbed.pl43 my $mate1 = "";
48 "1=s" => \$mate1,
71 my @mate1s = split(/,/, $mate1);
H A Dpe_verify.pl142 my $mate1 = ($l1rs[$#l1rs] eq "1");
143 my $mate1str = $mate1 ? "1" : "0";
169 if($mate1) { $pesFw++; } else { $pesRc++; }

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