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Searched refs:admix (Results 1 – 25 of 125) sorted by relevance

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/dports/biology/hhsuite/hh-suite-3.3.0/src/cs/
H A Dpseudocounts-inl.h33 AdmixToTargetNeff(seq, p, admix); in AddTo()
35 AdmixTo(seq, p, admix); in AddTo()
48 AdmixToTargetNeff(cp, p, admix); in AddTo()
50 AdmixTo(cp, p, admix); in AddTo()
60 double tau = admix(1.0); in AdmixTo()
72 double tau = admix(q.neff[i]); in AdmixTo()
90 AdmixTo(q, pp, admix); in AdmixToTargetNeff()
96 else r = admix.GetTargetNeffParam(); in AdmixToTargetNeff()
102 AdmixTo(q, p, admix); in AdmixToTargetNeff()
105 AdmixTo(q, p, admix); in AdmixToTargetNeff()
[all …]
H A Dpseudocounts.h133 Profile<Abc> AddTo(const Sequence<Abc>& seq, Admix& admix) const;
136 Profile<Abc> AddTo(const CountProfile<Abc>& cp, Admix& admix) const;
166 void AdmixTo(const Sequence<Abc>& q, Profile<Abc>& p, const Admix& admix) const;
169 void AdmixTo(const CountProfile<Abc>& q, Profile<Abc>& p, const Admix& admix) const;
173 double AdmixToTargetNeff(const T& q, Profile<Abc>& p, Admix& admix) const;
H A Dcstranslate_app.h556 CSBlastAdmix admix(opts_.pc_admix, opts_.pc_ali); in ReadProfile()
557 profile.counts = pc_->AddTo(profile, admix); in ReadProfile()
569 ConstantAdmix admix(opts_.pc_admix); in ReadProfile()
570 profile.counts = pc_->AddTo(seq, admix); in ReadProfile()
589 CSBlastAdmix admix(opts_.pc_admix, opts_.pc_ali); in ReadProfile()
590 profile.counts = pc_->AddTo(profile, admix); in ReadProfile()
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/VQSR/
H A DVQSR.mixedTest.input.vcf20 …InbreedingCoeff=0.0715;MQ=67.54;MQ0=0;MQRankSum=-0.549;QD=0.53;ReadPosRankSum=-13.245;set=EUR.admix
21 …InbreedingCoeff=0.0715;MQ=67.54;MQ0=0;MQRankSum=-0.549;QD=0.53;ReadPosRankSum=-13.245;set=EUR.admix
22 …InbreedingCoeff=0.0716;MQ=49.54;MQ0=22;MQRankSum=-5.327;QD=2.71;ReadPosRankSum=-8.146;set=ASN.admix
23 …InbreedingCoeff=0.0716;MQ=49.54;MQ0=22;MQRankSum=-5.327;QD=2.71;ReadPosRankSum=-8.146;set=ASN.admix
24 …nbreedingCoeff=0.2728;MQ=46.55;MQ0=85;MQRankSum=-6.417;QD=30.65;ReadPosRankSum=-2.058;set=EUR.admix
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/VQSR/expected/
H A DapplySNPAndIndelResult.vcf28 …54;MQ0=0;MQRankSum=-0.549;QD=0.53;ReadPosRankSum=-13.245;VQSLOD=-1.235e+00;culprit=FS;set=EUR.admix
29 …ankSum=-0.549;QD=0.53;ReadPosRankSum=-13.245;VQSLOD=-1.238e+00;culprit=HaplotypeScore;set=EUR.admix
30 …54;MQ0=22;MQRankSum=-5.327;QD=2.71;ReadPosRankSum=-8.146;VQSLOD=-5.678e-01;culprit=FS;set=ASN.admix
31 …RankSum=-5.327;QD=2.71;ReadPosRankSum=-8.146;VQSLOD=-5.534e-01;culprit=HaplotypeScore;set=ASN.admix
32 …Q=46.55;MQ0=85;MQRankSum=-6.417;QD=30.65;ReadPosRankSum=-2.058;VQSLOD=3.59;culprit=QD;set=EUR.admix
/dports/biology/hhsuite/hh-suite-3.3.0/src/
H A Dhhdecl.h113 : admix(m), pca(a), pcb(b), pcc(c), target_neff(neff) {} in admix() function
116 switch (admix) { in CreateAdmix()
131 Admix admix; // admixture mode member
H A Dhhdecl.cpp52 pc_hhm_context_engine.admix = Pseudocounts::HHsearchAdmix; in Parameters()
58 pc_prefilter_context_engine.admix = Pseudocounts::CSBlastAdmix; in Parameters()
H A Dhhmake.cpp96 …ition dependence of pc admixture 'tau' (pc mode, default=%-i) \n",par.pc_hhm_context_engine.admix); in help()
238 par.pc_hhm_context_engine.admix = (Pseudocounts::Admix) atoi(argv[++i]); in ProcessArguments()
312 …par.pc_hhm_context_engine.admix = (Pseudocounts::Admix) 0; // no amino acid and transition pseudoc… in main()
H A Dhhhmm.h85 cs::Admix* admix);
H A Dhhsearch.cpp170 …tion dependence of pc admixture 'tau' (pc mode, default=%-i) \n", par.pc_hhm_context_engine.admix); in help()
414 par.pc_hhm_context_engine.admix = (Pseudocounts::Admix) atoi( in ProcessArguments()
H A Dhhalign.cpp155 …tion dependence of pc admixture 'tau' (pc mode, default=%-i) \n", par.pc_hhm_context_engine.admix); in help()
440 par.pc_hhm_context_engine.admix = (Pseudocounts::Admix) atoi(argv[++i]); in ProcessArguments()
H A Dhhconsensus.cpp216 par.pc_hhm_context_engine.admix = (Pseudocounts::Admix) atoi(argv[++i]); in ProcessArguments()
H A Dhhblits.cpp333 …tion dependence of pc admixture 'tau' (pc mode, default=%-i) \n", par.pc_hhm_context_engine.admix); in help()
356 …ependence of pc admixture 'tau' (pc mode, default=%-i) \n", par.pc_prefilter_context_engine.admix); in help()
648 par.pc_hhm_context_engine.admix = (Pseudocounts::Admix) atoi(argv[++i]); in ProcessArguments()
657 par.pc_prefilter_context_engine.admix = (Pseudocounts::Admix) atoi( in ProcessArguments()
H A Dhhhmm.cpp1817 cs::Admix* admix) { in AddContextSpecificPseudocounts() argument
1818 if (has_pseudocounts || pc == NULL || admix == NULL) { in AddContextSpecificPseudocounts()
1827 cs::Profile<cs::AA> profile = pc->AddTo(cp, *admix); in AddContextSpecificPseudocounts()
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/varianteval/AlleleFrequencyQC/
H A Daf.thousand_genomes.10sites.vcf3 …admix/AFR.admix.phase1.chr1.42.raw.snps.vcf, /humgen/1kg/processing/production_wgs_phase1/consensu…
146 …MQ=68.54;MQ0=0;MQRankSum=1.120;QD=11.02;ReadPosRankSum=0.013;SB=-341.63;VQSLOD=5.3634;pop=AFR.admix
/dports/japanese/groff/groff-1.18.1.1/contrib/mm/examples/
H A DReferences351 admix
759 admix
907 admix
/dports/devel/clojure-cider/cider-1.1.0/
H A Dcider-cheatsheet.el504 (clojure.core.async admix solo-mode mix unmix unmix-all toggle merge pipe unique))
/dports/textproc/link-grammar/link-grammar-5.8.0/data/en/words/
H A Dwords-medical.v.4.131 admix.v
/dports/devel/sgb/sgb-20090810_1/
H A Dwords.dat59 admix+
/dports/net-mgmt/cowpatty/cowpatty-4.8/
H A Ddict3139 admix
/dports/www/py-nevow/Nevow-0.14.0/examples/files/
H A Dwords2701 admix
/dports/databases/db18/db-18.1.40/test/tcl/
H A Dwordlist4148 admix
/dports/databases/db5/db-5.3.28/test/tcl/
H A Dwordlist4148 admix
/dports/lang/fpc-source/fpc-3.2.2/tests/bench/shootout/io/
H A Drevfile.in705 admix
H A Drev.out10028 admix

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