| /dports/benchmarks/hpl/hpl-2.3/testing/ptest/ |
| H A D | HPL_pddriver.c | 99 inbm, indh, indv, ipfa, ipq, irfa, itop, local
181 for( indv = 0; indv < ndvs; indv++ )
187 algo.nbmin = nbmval[inbm]; algo.nbdiv = ndvval[indv];
|
| /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 $2
|
| /dports/biology/ddocent/dDocent-2.7.8/scripts/untested/ |
| H A D | filter_missing_ind.sh | 31 mawk -v x=$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 $2
|
| /dports/biology/ddocent/dDocent-2.7.8/scripts/untested/old/ |
| H A D | filter_lowdepth_ind.sh | 6 mawk -v x=$CUTOFF '$3 < x' $2.idepth | cut -f1 > lowDP.indv
8 vcftools --vcf $1 --remove lowDP.indv --recode --recode-INFO-all --out $2
|
| H A D | filter_missing_ind.sh | 31 mawk -v x=$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
|
| /dports/biology/ddocent/dDocent-2.7.8/tutorials/ |
| H A D | FilterTut | 97 #c#7 $vcftools --vcf raw.g5mac3dp3.recode.vcf --missing-indv
195 #c#10 $mawk '$5 > 0.5' out.imiss | cut -f1 > lowDP.indv
199 #c#11 $vcftools --vcf raw.g5mac3dp3.recode.vcf --remove lowDP.indv --recode --recode-INFO-all --out…
|
| H A D | Filtering Tutorial.md | 119 vcftools --vcf raw.g5mac3dp3.recode.vcf --missing-indv
227 mawk '$5 > 0.5' out.imiss | cut -f1 > lowDP.indv
234 vcftools --vcf raw.g5mac3dp3.recode.vcf --remove lowDP.indv --recode --recode-INFO-all --out raw.g5…
|
| /dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
| H A D | genotypeSummary.cpp | 20 struct indv{ struct
247 vector<indv *> countData; in main()
257 indv * dip = new indv; in main()
|
| H A D | splitUniqStarts.cpp | 20 struct indv{ struct
|
| /dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
| H A D | genotypeSummary.cpp | 20 struct indv{ struct
247 vector<indv *> countData; in main()
257 indv * dip = new indv; in main()
|
| H A D | splitUniqStarts.cpp | 20 struct indv{ struct
|
| /dports/biology/py-pysam/pysam-0.18.0/pysam/ |
| H A D | libchtslib.pxd | 2109 # @which: determine if INFO/AN,AC and indv fields be used
2115 # used (BCF_UN_INFO) and and if indv fields can be split (BCF_UN_FMT).
|
| /dports/biology/vcflib/vcflib-1.0.2/src/ |
| H A D | genotypeSummary.cpp | 29 struct indv{ struct
257 vector<indv *> countData; in main()
267 indv * dip = new indv; in main()
|
| H A D | splitUniqStarts.cpp | 29 struct indv{ struct
|
| /dports/biology/vcftools/vcftools-0.1.16/src/cpp/ |
| 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 …]
|
| 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 …]
|
| 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 …]
|
| H A D | bcf_file.cpp | 226 out << "\t" << meta_data.indv[ui]; in print()
281 header_str += meta_data.indv[ui]; in print_bcf()
|
| 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 …]
|
| 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 …]
|
| 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()
|
| H A D | header.cpp | 91 indv.push_back(tmp_str); in parse_header()
|
| H A D | header.h | 53 vector<string> indv; variable
|
| H A D | variant_file_diff.cpp | 39 combined_individuals[meta_data.indv[ui]] = make_pair<int,int>((int)ui, -1); in return_indv_union()
45 string indv_id = file2.meta_data.indv[ui]; in return_indv_union()
1449 indv_id = meta_data.indv[indv1]; in output_switch_error()
1451 indv_id = diff_variant_file.meta_data.indv[indv2]; in output_switch_error()
1490 indv_id = meta_data.indv[indv1]; in output_switch_error()
1492 indv_id = diff_variant_file.meta_data.indv[indv2]; in output_switch_error()
|
| H A D | variant_file_filters.cpp | 63 if (indv_to_keep_copy.find(meta_data.indv[ui]) == indv_to_keep_copy.end()) in filter_individuals_by_keep_list()
100 if (indv_to_exclude_copy.find(meta_data.indv[ui]) != indv_to_exclude_copy.end()) in filter_individuals_by_exclude_list()
|