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Searched refs:indv (Results 1 – 25 of 201) sorted by relevance

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/dports/biology/vcftools/vcftools-0.1.16/src/cpp/
H A Dvcf_entry_setters.cpp74 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()
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H A Dbcf_entry_setters.cpp193 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()
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H A Dbcf_entry.h39 …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);
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H A Dvcf_entry.h30 …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);
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H A Dentry_getters.cpp289 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()
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H A Dbcf_entry.cpp270 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()
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H A Dvcf_entry.cpp140 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()
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H A Dentry.h35 …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;
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H A Dentry_setters.cpp28 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()
/dports/math/R-cran-deldir/deldir/src/
H A Dcircen.f5 dimension indv(3)
36 indv(1) = i
37 indv(2) = j
38 indv(3) = k
39 call intpr("Point numbers:",-1,indv,3)
H A Dqtest1.f4 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)
/dports/math/cadabra2/cadabra2-2.3.6.8/core/
H A DCombinatorics.cc33 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()
/dports/math/R-cran-deldir/deldir/inst/SavedRatfor/
H A Dcircen.r8 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)
H A Dqtest1.r10 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)
/dports/math/R-cran-deldir/deldir/inst/ratfor/
H A Dcircen.r8 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)
H A Dqtest1.r10 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)
/dports/biology/ddocent/dDocent-2.7.8/scripts/untested/
H A Dfilter_missing_ind.sh31 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 $2
/dports/biology/ddocent/dDocent-2.7.8/scripts/untested/old/
H A Dfilter_missing_ind.sh31 mawk -v x=$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 $2
/dports/biology/ddocent/dDocent-2.7.8/scripts/
H A Dfilter_missing_ind.sh53 mawk -v x=$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
/dports/math/moab/fathomteam-moab-7bde9dfb84a8/examples/fortran/
H A DPushParMeshIntoMoabF90.F9050 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)
/dports/science/quantum-espresso/q-e-qe-6.7.0/CPV/examples/example01/reference/
H A Dsio2.cp.start.out235 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
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H A Dsio2.cp.restart.out241 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
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/dports/math/gismo/gismo-21.12.0/src/gsModeling/
H A DgsVolumeBlock.h477 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()
/dports/science/quantum-espresso/q-e-qe-6.7.0/CPV/examples/Restart_example/reference/
H A Dsio2.cp.restart.out241 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
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H A Dsio2.cp.start.out236 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
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