| /dports/biology/migrate/migrate-3.6.11/contribution/ |
| H A D | combine-sumfiles | 171 $locis[$zz] = $loci;
172 if($sumloci < $loci)
174 $sumloci = $loci;
180 $loci = $sumloci;
182 print "loci=$loci\n";
251 $locis[$zz] = $loci;
252 if($sumloci < $loci)
254 $sumloci = $loci;
260 $loci = $sumloci;
321 $sumloci += $loci;
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| H A D | mba | 56 @loci = split(' ', `grep \-v \\# $file | awk \'\{print \$2\} \' \| sort -n \| uniq`);
61 foreach $l (@loci)
73 foreach $l (@loci)
93 foreach $l (@loci)
126 @loci = split(' ', `grep \-v \\# $file | awk \'\{print \$2\} \' \| sort -n \| uniq`);
132 foreach $l (@loci)
145 foreach $l (@loci)
162 foreach $l (@loci)
170 foreach $l (@loci)
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| /dports/biology/mapm3/mapm3-3.0_1/mapm/ |
| H A D | two_cmds.c | 129 unarray(loci,int); in group()
169 array(loci,num_loci,int); in haplotype()
230 unarray(loci,int); in haplotype()
258 unarray(loci,int); in unhaplotype()
321 int a, b, n, num_loci, *loci=NULL; in biglods() local
339 unarray(loci,int); in biglods()
444 hold(more_mode) print_lodtable(loci,loci,num_loci,num_loci,type); in lodtable()
447 unarray(loci,int); in lodtable()
471 unarray(loci,int); in pairwise()
747 unarray(loci,int); in three_point()
[all …]
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| /dports/biology/stacks/stacks-2.4/src/ |
| H A D | sql_utilities.h | 138 if (loci.count(id) > 0) {
145 strcpy(loci[id]->model, parts[5].c_str());
151 loci[id]->depth++;
158 loci[id]->reads.push_back(read);
163 loci[id]->comp.push_back(read_id);
220 loci[c->id] = c;
307 if (loci.count(id) > 0) {
308 loci[id]->snps.push_back(snp);
370 if (loci.count(id) > 0) {
371 loci[id]->alleles[parts[2]] = atoi(parts[4].c_str());
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| H A D | export_formats.cc | 226 cloc = loci[i]->cloc; in write_batch()
505 loc = loci[j]; in write_batch_pairwise()
754 loc = loci[j]; in write_batch_pairwise()
797 loc = loci[j]; in write_batch_pairwise()
873 cloc = loci[i]->cloc; in write_batch()
886 Datum **d = loci[i]->d; in write_batch()
962 for (j = loci[i]->cloc->gmap.begin(); j != loci[i]->cloc->gmap.end(); j++) in write_batch()
1016 LocBin* loc = loci[i]; in write_batch()
1079 loc = loci[i]; in write_batch()
1152 loc = loci[i]; in write_batch()
[all …]
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| /dports/biology/ddocent/dDocent-2.7.8/scripts/untested/ |
| H A D | dup_sample_filter.sh | 30 …cut -f1,2,10 | cut -f1 -d ":") | mawk '$3 != $6' | mawk '!/\./' | cut -f1,2 > bad.loci.${NAMES[$i]}
34 cat bad.loci.${NAMES[0]} > total.bad.loci
39 cat bad.loci.${NAMES[$i]} >> total.bad.loci
44 cat total.bad.loci | perl -e 'while (<>) {chomp; $z{$_}++;} while(($k,$v) = each(%z)) {print "$v\t$…
45 rm total.bad.loci
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| /dports/biology/migrate/migrate-3.6.11/src/ |
| H A D | migevents.c | 85 for(locus=0; locus < world->loci; locus++) in destroy_mighist()
128 const long loci1 = ((world->loci == 1) ? 1 : world->loci + 1); in print_mighist_output()
130 const long sumloc = ((world->loci == 1) ? 0 : world->loci); in print_mighist_output()
183 for (locus = 0; locus < world->loci; locus++) in print_mighist_output()
277 if (locus != world->loci) in print_mighist_output()
499 for(i=0;i<world->numpop2*world->loci;i++) in read_event_values_fromfile()
585 if(world->loci>1) in print_event_values_tofile()
632 for(locus=0; locus < world->loci; locus++) in prepare_event_values()
694 for (locus = 0; locus < world->loci; locus++) in prepare_event_values()
734 long sumloc = (world->loci > 1) ? 1 : 0; in print_event_values()
[all …]
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| H A D | data.c | 159 long loci = data->loci; in destroy_data() local
184 for(locus=0; locus < loci; locus++) in destroy_data()
218 for(locus=0;locus<data->loci;locus++) in destroy_data()
529 long loci = (*data)->loci; in init_data_structure1() local
557 (*data)->numdatatypealloc = loci; in init_data_structure1()
558 (*data)->numsublocialloc = loci; in init_data_structure1()
563 for(locus=0;locus<loci;locus++) in init_data_structure1()
906 for(i = 0 ; i < data->loci; i++) in read_sites()
1218 if(data->loci>1) in read_popheader()
2089 data->loci); in print_data_summary()
[all …]
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| H A D | skyline.c | 379 for (locus = 0; locus < world->loci; locus++) in setup_expected_events()
406 for (locus = 0; locus < world->loci; locus++) in destroy_expected_events()
469 for(i=0;i<world->numpop2*world->loci;i++) in read_expected_values_fromfile()
560 if(world->loci>1) in print_expected_values_tofile()
570 for(locus=0; locus < world->loci + sumloc; locus++) in print_expected_values_tofile()
609 for(locus=0; locus < world->loci; locus++) in prepare_expected_values()
685 if(world->loci>1) in prepare_expected_values()
698 for (locus = 0; locus < world->loci; locus++) in prepare_expected_values()
754 long sumloc = (world->loci > 1) ? 1 : 0; in print_expected_values()
773 for(locus=0; locus < world->loci+sumloc; locus++) in print_expected_values()
[all …]
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| H A D | world.c | 490 (boolean *) mycalloc (1, sizeof (boolean) * (data->loci + 1 + data->loci)); in fill_worlddata()
589 world->loci = data->loci; in init_world()
1063 long loci = world->loci; in plot_surface() local
1102 if (world->loci == 1) in plot_surface()
1126 1) ? loci : 0) : loci; in plot_surface()
1215 long g, a, loci = world->loci; in print_alpha_curve() local
1644 for(i=0;i<world->loci;i++) in free_world()
2780 long loci = world->loci; in print_fst() local
2782 if (loci < 40) in print_fst()
4037 kopie->loci = original->loci; in klone()
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| H A D | migrate_mpi.h | 89 extern void mpi_runloci_master (long loci, int *who, world_fmt *world, boolean options_readsum, boo…
158 long repstart, long repstop, long loci, long kind,
174 mpi_broadcast_results (world_fmt * world, long loci,
182 long repstart, long repstop, long loci,
184 extern long mpi_send_stop_mcmc_lociworker(long numcpu, long loci);
185 extern long mpi_send_stop_mcmc_worker_orig(long numcpu, long loci, MPI_Comm *comm, MPI_Request *ir…
187 extern long mpi_send_stop_mcmc_replicateworker(long numcpu, long loci);
188 extern int get_replicant_color(int numcpu, long maxreplicate, long loci);
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| H A D | histogram.c | 87 sscanf (input+3, "%li %li %li %li %li %i", &world->loci, &world->numpop, in read_from_bayesmdim_minimal_info()
89 printf("%i> loci = %li\n",myID, world->loci); in read_from_bayesmdim_minimal_info()
119 options->muloci = data->loci = world->loci; in read_from_bayesmdim_minimal_info()
122 sizeof (boolean) * (data->loci + 1)); in read_from_bayesmdim_minimal_info()
123 memset (data->skiploci, 0, sizeof (boolean) * (data->loci + 1)); in read_from_bayesmdim_minimal_info()
146 for(i = world->numpop2; i < world->numpop2+world->bayes->mu * world->loci; i++) in get_fullbinsum()
206 done = (boolean *) mycalloc(world->loci, sizeof(boolean)); in read_bayes_fromfile()
209 autocorrelation = (MYREAL *) mycalloc(2 * world->loci * nn, sizeof(MYREAL)); in read_bayes_fromfile()
210 ess = autocorrelation + world->loci * nn; in read_bayes_fromfile()
213 n = (long *) mycalloc(numpop2 + world->bayes->mu * world->loci, sizeof(long)); in read_bayes_fromfile()
[all …]
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| /dports/biology/recombine/recombine1.41/ |
| H A D | jworld.c | 70 long loci; in plot_surface() local
72 loci = getdata_numloci(op,data); in plot_surface()
90 lowcus = loci; in plot_surface()
109 for (i = 1; i < loci + 1; i++) {
113 create_nr(nr, atl[loci].numpop, g);
185 nr->param[4] = world->atl[loci + 1].param[4];
193 nr->param[1] = world->atl[loci + 1].param[1];
195 nr->param[3] = world->atl[loci + 1].param[3];
202 nr->param[0] = world->atl[loci + 1].param[0];
207 nr->param[0] = world->atl[loci + 1].param[0];
[all …]
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| /dports/devel/cmake/cmake-3.22.1/Tests/Complex/ |
| H A D | CMakeLists.txt | 43 …loci/0\\.075\\.model_cassisi_eos1_10$;^C:/hoffman/My Builds/testcase/www/eospaper/eff_fit/rho-T-lo…
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| /dports/devel/cmake/cmake-3.22.1/Tests/ComplexOneConfig/ |
| H A D | CMakeLists.txt | 36 …loci/0\\.075\\.model_cassisi_eos1_10$;^C:/hoffman/My Builds/testcase/www/eospaper/eff_fit/rho-T-lo…
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| /dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/src/ |
| H A D | gff_utils.cpp | 28 if (loci[0]->start>x) return 0; in qsearch_gloci()
29 if (loci.Last()->start<x) return -1; in qsearch_gloci()
33 int maxh=loci.Count()-1; in qsearch_gloci()
38 istart=loci[i]->start; in qsearch_gloci()
52 while (idx<=maxh && loci[idx]->start<=x) { in qsearch_gloci()
406 if (gdata->loci.Count()==0) { in placeGf()
407 gdata->loci.Add(new GffLocus(t)); in placeGf()
425 gdata->loci.Add(new GffLocus(t)); in placeGf()
434 GffLocus& loc=*(gdata->loci[l]); in placeGf()
509 gdata->loci.Swap(i,i+1); in placeGf()
[all …]
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| /dports/devel/avr-gdb/gdb-7.3.1/gdb/testsuite/gdb.trace/ |
| H A D | unavailable.cc | 212 int loci = 12; in local_test_func() local
230 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in local_test_func()
241 register int loci = 12; in reglocal_test_func() local
258 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in reglocal_test_func()
269 static int loci; in statlocal_test_func() local
277 loci = 12; in statlocal_test_func()
290 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in statlocal_test_func()
294 loci = 0; in statlocal_test_func()
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| H A D | collection.c | 100 int loci = 12; in local_test_func() local
118 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in local_test_func()
126 register int loci = 12; in reglocal_test_func() local
143 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in reglocal_test_func()
151 static int loci; in statlocal_test_func() local
159 loci = 12; in statlocal_test_func()
172 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in statlocal_test_func()
176 loci = 0; in statlocal_test_func()
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| /dports/devel/gdb761/gdb-7.6.1/gdb/testsuite/gdb.trace/ |
| H A D | unavailable.cc | 211 int loci = 12; in local_test_func() local
229 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in local_test_func()
240 register int loci = 12; in reglocal_test_func() local
257 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in reglocal_test_func()
268 static int loci; in statlocal_test_func() local
276 loci = 12; in statlocal_test_func()
289 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in statlocal_test_func()
293 loci = 0; in statlocal_test_func()
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| /dports/devel/gdb/gdb-11.1/gdb/testsuite/gdb.trace/ |
| H A D | unavailable.cc | 211 int loci = 12; in local_test_func() local
229 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in local_test_func()
240 register int loci = 12; in reglocal_test_func() local
257 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in reglocal_test_func()
268 static int loci; in statlocal_test_func() local
276 loci = 12; in statlocal_test_func()
289 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in statlocal_test_func()
293 loci = 0; in statlocal_test_func()
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| /dports/editors/texmacs/TeXmacs-1.99.4-src/src/Data/Observers/ |
| H A D | link.cpp | 96 while (!is_nil (loci)) { in ~link_repository_rep()
97 tree t= obtain_tree (loci->item); in ~link_repository_rep()
98 unregister_pointer (ids->item, loci->item); in ~link_repository_rep()
99 detach_observer (t, loci->item); in ~link_repository_rep()
101 loci= loci->next; in ~link_repository_rep()
115 loci= list<observer> (obs, loci); in insert_locus()
124 loci= list<observer> (obs, loci); in insert_locus()
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| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Depictor/ |
| H A D | testDepictor.cpp | 143 locj -= loci; in testCollisions()
388 locj -= loci; in testIssue248()
420 locj -= loci; in testQueries()
503 xx += loci.x * loci.x; in testIssue2821647()
504 yy += loci.y * loci.y; in testIssue2821647()
517 xx += loci.x * loci.x; in testIssue2821647()
518 yy += loci.y * loci.y; in testIssue2821647()
531 xx += loci.x * loci.x; in testIssue2821647()
532 yy += loci.y * loci.y; in testIssue2821647()
545 xx += loci.x * loci.x; in testIssue2821647()
[all …]
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| /dports/devel/zpu-binutils/zpu-toolchain-1.0/toolchain/gdb/gdb/testsuite/gdb.trace/ |
| H A D | collection.c | 90 int loci = 12; in local_test_func() local
107 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in local_test_func()
115 register int loci = 12; in reglocal_test_func() local
132 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in reglocal_test_func()
140 static int loci; in statlocal_test_func() local
148 loci = 12; in statlocal_test_func()
161 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in statlocal_test_func()
165 loci = 0; in statlocal_test_func()
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| /dports/devel/zpu-gcc/zpu-toolchain-1.0/toolchain/gdb/gdb/testsuite/gdb.trace/ |
| H A D | collection.c | 90 int loci = 12; in local_test_func() local
107 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in local_test_func()
115 register int loci = 12; in reglocal_test_func() local
132 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in reglocal_test_func()
140 static int loci; in statlocal_test_func() local
148 loci = 12; in statlocal_test_func()
161 (int) locc + loci + locf + locd + locst.memberi + locar[1]; in statlocal_test_func()
165 loci = 0; in statlocal_test_func()
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| /dports/biology/lamarc/lamarc-2.1.8/src/guiconv/ |
| H A D | gc_assigntab.cpp | 444 constObjVector loci = st.GetConstDisplayableLociInMapOrderFor(regionId); in MakeContent() local
447 if(loci.size() == 0) in MakeContent()
456 … dds->AddRegion(new gcRegionCell(newPanel,group),locusIndex,locusIndex+loci.size()-1); in MakeContent()
460 for(constObjVector::const_iterator liter=loci.begin(); liter != loci.end(); liter++) in MakeContent()
495 if(blockVec.empty() && (loci.size() == 1)) in MakeContent()
497 …e("AddPanel Empty cell row: %i column: %i length: %i", dispIndex,locusIndex+1+offset, loci.size()); in MakeContent()
518 … dds->AddPanel(new gcPanelCell(newPanel, panel), dispIndex, locusIndex+1, loci.size()); in MakeContent()
551 if(blockVec.empty() && (loci.size() == 1)) in MakeContent()
567 … dds->AddPanel(new gcPanelCell(newPanel, panel), dispIndex, locusIndex+1, loci.size()); in MakeContent()
597 if(blockVec.empty() && (loci.size() == 1)) in MakeContent()
[all …]
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