/dports/biology/vcftools/vcftools-0.1.16/src/cpp/ |
H A D | vcf_entry_setters.cpp | 74 ploidy[indv] = 2; in set_indv_GENOTYPE_and_PHASE() 83 ploidy[indv] = 2; in set_indv_GENOTYPE_and_PHASE() 89 ploidy[indv] = 1; in set_indv_GENOTYPE_and_PHASE() 100 parsed_GT[indv] = true; in set_indv_GENOTYPE_and_PHASE() 106 ploidy[indv] = 2; in set_indv_GENOTYPE_and_PHASE() 115 ploidy[indv] = 2; in set_indv_GENOTYPE_and_PHASE() 134 GENOTYPE[indv] = a; in set_indv_GENOTYPE_alleles() 151 GENOTYPE[indv] = a; in set_indv_GENOTYPE_alleles() 159 GENOTYPE[indv] = in; in set_indv_GENOTYPE_ids() 167 PHASE[indv] = in; in set_indv_PHASE() [all …]
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H A D | bcf_entry_setters.cpp | 193 ploidy[indv] = 0; in set_indv_GENOTYPE_and_PHASE() 200 ploidy[indv]++; in set_indv_GENOTYPE_and_PHASE() 204 if (ploidy[indv] == 0) in set_indv_GENOTYPE_and_PHASE() 283 GENOTYPE[indv] = in; in set_indv_GENOTYPE_alleles() 291 GENOTYPE[indv] = in; in set_indv_GENOTYPE_ids() 299 PHASE[indv] = in; in set_indv_PHASE() 312 GQUALITY[indv] = -1; in set_indv_GQUALITY() 320 GQUALITY[indv] = tmp; in set_indv_GQUALITY() 329 GQUALITY[indv] = -1; in set_indv_GQUALITY() 336 GQUALITY[indv] = 99; in set_indv_GQUALITY() [all …]
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H A D | bcf_entry.h | 39 …void set_indv_GENOTYPE_and_PHASE(unsigned int indv, const pair<string, string> &genotype, char pha… 40 void set_indv_GENOTYPE_and_PHASE(unsigned int indv, const pair<int, int> &genotype, char phase); 42 void set_indv_GENOTYPE_ids(unsigned int indv, const pair<int, int> &in); 43 void set_indv_GQUALITY(unsigned int indv, const vector<char> &in); 44 void set_indv_GQUALITY(unsigned int indv, const float &in); 45 void set_indv_GFILTER(unsigned int indv, const string &in); 46 void set_indv_GFILTER(unsigned int indv, const vector<char> &in); 47 void set_indv_PHASE(unsigned int indv, char in); 48 void set_indv_GENOTYPE_alleles(unsigned int indv, const pair<int, int> &in); 52 void read_indv_generic_entry(unsigned int indv, const string &FORMAT_id, string &out); [all …]
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H A D | vcf_entry.h | 30 …void parse_genotype_entry(unsigned int indv, bool GT=false, bool GQ=false, bool DP=false, bool FT=… 35 void read_indv_generic_entry(unsigned int indv, const string &FORMAT_id, string &out); 44 void set_indv_GENOTYPE_and_PHASE(unsigned int indv, const string &in); 45 …void set_indv_GENOTYPE_and_PHASE(unsigned int indv, const pair<string, string> &genotype, char pha… 46 void set_indv_GENOTYPE_and_PHASE(unsigned int indv, const pair<int, int> &genotype, char phase); 47 void set_indv_GENOTYPE_alleles(unsigned int indv, const pair<string, string> &in); 48 void set_indv_GENOTYPE_alleles(unsigned int indv, char a1, char a2); 49 void set_indv_GENOTYPE_ids(unsigned int indv, const pair<int, int> &in); 50 void set_indv_PHASE(unsigned int indv, char in); 51 void set_indv_GQUALITY(unsigned int indv, double in); [all …]
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H A D | entry_getters.cpp | 289 assert(parsed_GT[indv] == true); in get_indv_GENOTYPE_strings() 300 assert(parsed_GT[indv] == true); in get_indv_GENOTYPE_ids() 301 out = GENOTYPE[indv]; in get_indv_GENOTYPE_ids() 306 assert(parsed_GT[indv] == true); in get_indv_PHASE() 307 return PHASE[indv]; in get_indv_PHASE() 315 return DEPTH[indv]; in get_indv_DEPTH() 323 return GQUALITY[indv]; in get_indv_GQUALITY() 330 out = GFILTER[indv]; in get_indv_GFILTER_vector() 346 out += GFILTER[indv][ui]; in get_indv_GFILTER() 355 assert (parsed_GT[indv]==true); in get_indv_ploidy() [all …]
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H A D | bcf_entry.cpp | 270 set_indv_GQUALITY(indv, tmp); in parse_genotype_entry() 304 set_indv_DEPTH(indv, tmp); in parse_genotype_entry() 313 set_indv_GFILTER(indv, tmp); in parse_genotype_entry() 320 if (GT && (parsed_GT[indv] == false)) in parse_genotype_entry() 324 if (GQ && (parsed_GQ[indv] == false)) in parse_genotype_entry() 326 set_indv_GQUALITY(indv, -1); in parse_genotype_entry() 328 if (DP && (parsed_DP[indv] == false)) in parse_genotype_entry() 330 set_indv_DEPTH(indv, -1); in parse_genotype_entry() 334 set_indv_GFILTER(indv, ""); in parse_genotype_entry() 358 parse_genotype_entry(indv, true); in read_indv_generic_entry() [all …]
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H A D | vcf_entry.cpp | 140 set_indv_GENOTYPE_and_PHASE(indv, tmpstr); in parse_genotype_entry() 158 set_indv_GFILTER(indv, tmpstr); in parse_genotype_entry() 190 set_indv_GFILTER(indv, tmpstr); in parse_genotype_entry() 196 if (GT && (parsed_GT[indv] == false)) in parse_genotype_entry() 200 if (GQ && (parsed_GQ[indv] == false)) in parse_genotype_entry() 202 set_indv_GQUALITY(indv, -1); in parse_genotype_entry() 204 if (DP && (parsed_DP[indv] == false)) in parse_genotype_entry() 206 set_indv_DEPTH(indv, -1); in parse_genotype_entry() 208 if (FT && (parsed_FT[indv] == false)) in parse_genotype_entry() 210 set_indv_GFILTER(indv, ""); in parse_genotype_entry() [all …]
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H A D | entry.h | 35 …virtual void parse_genotype_entry(unsigned int indv, bool GT=false, bool GQ=false, bool DP=false, … 84 void get_indv_GENOTYPE_ids(unsigned int indv, pair<int, int> &out) const; 85 void get_indv_GENOTYPE_strings(unsigned int indv, pair<string, string> &out) const; 86 char get_indv_PHASE(unsigned int indv) const; 87 double get_indv_GQUALITY(unsigned int indv) const; 88 int get_indv_DEPTH(unsigned int indv) const; 89 void get_indv_GFILTER(unsigned int indv, string &out) const; 90 void get_indv_GFILTER_vector(unsigned int indv, vector<string> &out) const; 91 int get_indv_ploidy(unsigned int indv) const; 96 virtual void read_indv_generic_entry(unsigned int indv, const string &FORMAT_id, string &out) = 0; [all …]
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H A D | entry_setters.cpp | 28 void entry::set_indv_DEPTH(unsigned int indv, int in) in set_indv_DEPTH() argument 30 parsed_DP[indv] = true; in set_indv_DEPTH() 34 DEPTH[indv] = -1; in set_indv_DEPTH() 40 DEPTH[indv] = in; in set_indv_DEPTH()
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/dports/math/R-cran-deldir/deldir/src/ |
H A D | circen.f | 5 dimension indv(3) 36 indv(1) = i 37 indv(2) = j 38 indv(3) = k 39 call intpr("Point numbers:",-1,indv,3)
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H A D | qtest1.f | 4 dimension x(-3:ntot), y(-3:ntot), xt(3), yt(3), indv(3) 34 indv(1) = i 35 indv(2) = j 36 indv(3) = k 39 call intpr("now, other vertex, nxt:",-1,indv,3)
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/dports/math/cadabra2/cadabra2-2.3.6.8/core/ |
H A D | Combinatorics.cc | 33 const combin::range_vector_t& indv, in determine_intersection_ranges() argument 38 for(unsigned int k=0; k<indv.size(); ++k) { // all ranges in indv in determine_intersection_ranges() 41 for(unsigned int kc=0; kc<indv[k].size(); ++kc) { in determine_intersection_ranges() 42 if(prod[i][ic] == indv[k][kc]) in determine_intersection_ranges() 43 newrange.push_back(indv[k][kc]); in determine_intersection_ranges()
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/dports/math/R-cran-deldir/deldir/inst/SavedRatfor/ |
H A D | circen.r | 8 dimension indv(3) # To facillitate a lucid error message. 47 indv(1) = i 48 indv(2) = j 49 indv(3) = k 50 call intpr("Point numbers:",-1,indv,3)
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H A D | qtest1.r | 10 dimension x(-3:ntot), y(-3:ntot), xt(3), yt(3), indv(3) 65 indv(1) = i 66 indv(2) = j 67 indv(3) = k 69 call intpr("now, other vertex, nxt:",-1,indv,3)
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/dports/math/R-cran-deldir/deldir/inst/ratfor/ |
H A D | circen.r | 8 dimension indv(3) # To facillitate a lucid error message. 50 indv(1) = i 51 indv(2) = j 52 indv(3) = k 53 call intpr("Point numbers:",-1,indv,3)
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H A D | qtest1.r | 10 dimension x(-3:ntot), y(-3:ntot), xt(3), yt(3), indv(3) 71 indv(1) = i 72 indv(2) = j 73 indv(3) = k 76 call intpr("now, other vertex, nxt:",-1,indv,3)
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/dports/biology/ddocent/dDocent-2.7.8/scripts/untested/ |
H A D | filter_missing_ind.sh | 31 mawk -v x=$CUTOFF '$5 > x' $2.imiss | cut -f1 > lowDP.indv 33 vcftools --vcf $1 --remove lowDP.indv --recode --recode-INFO-all --out $2 41 mawk -v x=$CUTOFF2 '$5 > x' $2.imiss | cut -f1 > lowDP.indv 43 vcftools --vcf $1 --remove lowDP.indv --recode --recode-INFO-all --out $2
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/dports/biology/ddocent/dDocent-2.7.8/scripts/untested/old/ |
H A D | filter_missing_ind.sh | 31 mawk -v x=$CUTOFF '$5 > x' $2.imiss | cut -f1 > lowDP.indv 33 vcftools --vcf $1 --remove lowDP.indv --recode --recode-INFO-all --out $2 41 mawk -v x=$CUTOFF2 '$5 > x' $2.imiss | cut -f1 > lowDP.indv 43 vcftools --vcf $1 --remove lowDP.indv --recode --recode-INFO-all --out $2
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/dports/biology/ddocent/dDocent-2.7.8/scripts/ |
H A D | filter_missing_ind.sh | 53 mawk -v x=$CUTOFF '$5 > x' $2.imiss | cut -f1 > lowDP.indv 55 vcftools --vcf $1 --remove lowDP.indv --recode --recode-INFO-all --out $2 67 mawk -v x=$CUTOFF2 '$5 > x' $2.imiss | cut -f1 > lowDP.indv 69 vcftools --vcf $1 --remove lowDP.indv --recode --recode-INFO-all --out $2
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/dports/math/moab/fathomteam-moab-7bde9dfb84a8/examples/fortran/ |
H A D | PushParMeshIntoMoabF90.F90 | 50 integer ic, ie, iv, istart, iend, ierr, indv, lnume, rank, sz 104 indv = iconn(lvpe*ie + iv) 105 if (lvids(indv) .eq. -1) then 108 lcoords(3*lnumv+ic) = coords(3*indv+ic) 110 lvids(indv) = lnumv 111 gvids(lnumv) = 1+indv 113 lconn(lvpe*(ie-istart)+iv) = lvids(indv)
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/dports/science/quantum-espresso/q-e-qe-6.7.0/CPV/examples/example01/reference/ |
H A D | sio2.cp.start.out | 235 1 indv= 1 ang. mom= 0 236 2 indv= 2 ang. mom= 0 237 3 indv= 3 ang. mom= 1 238 4 indv= 3 ang. mom= 1 239 5 indv= 3 ang. mom= 1 240 6 indv= 4 ang. mom= 1 241 7 indv= 4 ang. mom= 1 242 8 indv= 4 ang. mom= 1 251 1 indv= 1 ang. mom= 0 252 2 indv= 2 ang. mom= 1 [all …]
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H A D | sio2.cp.restart.out | 241 1 indv= 1 ang. mom= 0 242 2 indv= 2 ang. mom= 0 243 3 indv= 3 ang. mom= 1 244 4 indv= 3 ang. mom= 1 245 5 indv= 3 ang. mom= 1 246 6 indv= 4 ang. mom= 1 247 7 indv= 4 ang. mom= 1 248 8 indv= 4 ang. mom= 1 257 1 indv= 1 ang. mom= 0 258 2 indv= 2 ang. mom= 1 [all …]
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/dports/math/gismo/gismo-21.12.0/src/gsModeling/ |
H A D | gsVolumeBlock.h | 477 for (int indv = 0; indv != n - 2; indv++) variable 483 params3D(second, column) = params1D(indv + 1); 485 points.col(column) = cpPoints.col(indv * (n - 2) + indu); 554 for (int indv = 1; indv != n - 1; indv++) // ommit boundary in modifiedCoonsPatch() local 556 T v = params1D[indv]; in modifiedCoonsPatch() 572 vec = (1 - u) * values[3].col(indv) + in modifiedCoonsPatch() 573 u * values[1].col(indv); in modifiedCoonsPatch() 577 vec = (1 - u) * values[1].col(indv) + in modifiedCoonsPatch() 578 u * values[3].col(indv); in modifiedCoonsPatch()
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/dports/science/quantum-espresso/q-e-qe-6.7.0/CPV/examples/Restart_example/reference/ |
H A D | sio2.cp.restart.out | 241 1 indv= 1 ang. mom= 0 242 2 indv= 2 ang. mom= 0 243 3 indv= 3 ang. mom= 1 244 4 indv= 3 ang. mom= 1 245 5 indv= 3 ang. mom= 1 246 6 indv= 4 ang. mom= 1 247 7 indv= 4 ang. mom= 1 248 8 indv= 4 ang. mom= 1 257 1 indv= 1 ang. mom= 0 258 2 indv= 2 ang. mom= 1 [all …]
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H A D | sio2.cp.start.out | 236 1 indv= 1 ang. mom= 0 237 2 indv= 2 ang. mom= 0 238 3 indv= 3 ang. mom= 1 239 4 indv= 3 ang. mom= 1 240 5 indv= 3 ang. mom= 1 241 6 indv= 4 ang. mom= 1 242 7 indv= 4 ang. mom= 1 243 8 indv= 4 ang. mom= 1 252 1 indv= 1 ang. mom= 0 253 2 indv= 2 ang. mom= 1 [all …]
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