Home
last modified time | relevance | path

Searched refs:bedfile (Results 1 – 25 of 35) sorted by relevance

12

/dports/biology/plink/plink-ng-79b2df8c/1.9/
H A Dplink_ld.h132 int32_t ld_prune(Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t…
134 int32_t flipscan(Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_t…
136 int32_t ld_report(pthread_t* threads, Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t…
138 int32_t show_tags(Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintptr_…
140 int32_t haploview_blocks(Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, u…
142 int32_t twolocus(Epi_info* epi_ip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, uintpt…
144 int32_t epistasis_report(pthread_t* threads, Epi_info* epi_ip, FILE* bedfile, uintptr_t bed_offset,…
146 int32_t indep_pairphase(Ld_info* ldip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, ui…
150 int32_t test_mishap(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, double o…
154 int32_t set_test_common_init(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname…
[all …]
H A Dplink_assoc.h32 int32_t model_assoc(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname, char* o…
34 int32_t qassoc(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname, char* outnam…
36 int32_t gxe_assoc(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, double out…
38 int32_t testmiss(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname, char* outn…
40 int32_t cmh_assoc(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname, char* out…
42 int32_t cmh2_assoc(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, double ou…
44 int32_t homog_assoc(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, double o…
H A Dplink_calc.h58 int32_t calc_genome(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, uint32_t marker_ct, ui…
62 …uint32_t parallel_tot, uint64_t calculation_type, Rel_info* relip, FILE* bedfile, uintptr_t bed_of…
65 int32_t calc_pca(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, uint64_t ca…
68 …(pthread_t* threads, uint32_t parallel_idx, uint32_t parallel_tot, FILE* bedfile, uintptr_t bed_of…
70 int32_t calc_cluster_neighbor(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, uint32_t mar…
H A Dplink_family.h74 int32_t mendel_error_scan(Family_info* fam_ip, FILE* bedfile, uintptr_t bed_offset, char* outname, …
103 int32_t tdt(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_e…
105 int32_t dfam(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_…
107 int32_t qfam(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_…
109 int32_t make_pseudocontrols(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, …
H A Dplink_lasso.c119 if (fseeko(bedfile, bed_offset, SEEK_SET)) { in lasso_bigmem()
164 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in lasso_bigmem()
173 …le_valid_ct, pheno_nm2, final_mask, IS_SET(marker_reverse, marker_uidx), bedfile, loadbuf_raw, loa… in lasso_bigmem()
392 …nfiltered_sample_ct, sample_valid_ct, pheno_nm2, final_mask, do_reverse, bedfile, loadbuf_raw, loa… in load_and_normalize()
518 if (fseeko(bedfile, bed_offset, SEEK_SET)) { in lasso_lambda()
525 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in lasso_lambda()
690 if (fseeko(bedfile, bed_offset, SEEK_SET)) { in lasso_smallmem()
758 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in lasso_smallmem()
866 if (fseeko(bedfile, bed_offset, SEEK_SET)) { in lasso_smallmem()
872 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in lasso_smallmem()
[all …]
H A Dplink_misc.h88 int32_t write_stratified_freqs(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_en…
90 int32_t write_cc_freqs(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, uint3…
94 int32_t sexcheck(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, uintptr_t u…
102 int32_t het_report(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, uint32_t …
104 int32_t fst_report(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, uintptr_t…
106 int32_t score_report(Score_info* sc_ip, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct, u…
H A Dplink_glm.h31 int32_t glm_linear_assoc(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname, ch…
34 int32_t glm_logistic_assoc(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname, …
37 int32_t glm_linear_nosnp(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname, ch…
40 int32_t glm_logistic_nosnp(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname, …
H A Dplink_lasso.h21 …2_t hh_or_mt_exists, uint32_t lasso_lambda_iters, double lasso_h2, FILE* bedfile, char* outname, c…
23 int32_t lasso(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname…
H A Dplink_filter.h57 int32_t load_oblig_missing(FILE* bedfile, uintptr_t bed_offset, uintptr_t unfiltered_marker_ct, uin…
63 int32_t mind_filter(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname_end, double m…
65 int32_t calc_freqs_and_hwe(FILE* bedfile, char* outname, char* outname_end, uintptr_t unfiltered_ma…
67 int32_t write_missingness_reports(FILE* bedfile, uintptr_t bed_offset, char* outname, char* outname…
H A Dplink_rserve.h21 …ugin_host_or_socket, int32_t rplugin_port, uint32_t rplugin_debug, FILE* bedfile, uintptr_t bed_of…
H A Dplink_ld.c980 if (fseeko(bedfile, bed_offset + (uii * ((uint64_t)unfiltered_sample_ct4)), SEEK_SET)) { in ld_prune()
1683 if (fseeko(bedfile, bed_offset + (marker_uidx * ((uint64_t)unfiltered_sample_ct4)), SEEK_SET)) { in flipscan()
1697 if (load_raw(unfiltered_sample_ct4, bedfile, loadbuf_raw)) { in flipscan()
1762 if (fseeko(bedfile, bed_offset + (marker_uidx * ((uint64_t)unfiltered_sample_ct4)), SEEK_SET)) { in flipscan()
2387 … if (fseeko(bedfile, bed_offset + (marker_uidx1 * ((uint64_t)unfiltered_sample_ct4)), SEEK_SET)) { in ld_report_matrix()
2441 if (fseeko(bedfile, bed_offset + (marker_uidx2 * ((uint64_t)unfiltered_sample_ct4)), SEEK_SET)) { in ld_report_matrix()
2805 if (bedfile) { in load_and_split3()
2807 if (load_raw(unfiltered_sample_ct4, bedfile, rawbuf)) { in load_and_split3()
9540 if (fseeko(bedfile, bed_offset + (marker_uidx * ((uint64_t)unfiltered_sample_ct4)), SEEK_SET)) { in epistasis_report()
10555 if (fseeko(bedfile, bed_offset + (uljj * ((uint64_t)unfiltered_sample_ct4)), SEEK_SET)) { in indep_pairphase()
[all …]
H A Dplink_rserve.c33 …ugin_host_or_socket, int32_t rplugin_port, uint32_t rplugin_debug, FILE* bedfile, uintptr_t bed_of… in rserve_call() argument
280 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in rserve_call()
293 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in rserve_call()
297 … pheno_nm_ct, pheno_nm, final_mask, IS_SET(marker_reverse, marker_uidx), bedfile, loadbuf_raw, ulp… in rserve_call()
H A Dplink_homozyg.h44 int32_t calc_homozyg(Homozyg_info* hp, FILE* bedfile, uintptr_t bed_offset, uint32_t marker_ct, uin…
H A Dplink_homozyg.c877 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in populate_roh_slots_from_disk()
885 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in populate_roh_slots_from_disk()
889 if (load_raw(unfiltered_sample_ct4, bedfile, rawbuf)) { in populate_roh_slots_from_disk()
1826 …if (fseeko(bedfile, bed_offset + ((uint64_t)lookahead_end_uidx) * unfiltered_sample_ct4, SEEK_SET)… in roh_pool()
1836 …if (fseeko(bedfile, bed_offset + ((uint64_t)lookahead_end_uidx) * unfiltered_sample_ct4, SEEK_SET)… in roh_pool()
1843 if (load_raw(unfiltered_sample_ct4, bedfile, &(lookahead_buf[ulii * unfiltered_sample_ctl2]))) { in roh_pool()
2561 if (fseeko(bedfile, bed_offset, SEEK_SET)) { in calc_homozyg()
2573 if (fseeko(bedfile, bed_offset + (uint64_t)marker_uidx * unfiltered_sample_ct4, SEEK_SET)) { in calc_homozyg()
2595 if (fseeko(bedfile, bed_offset + (uint64_t)marker_uidx * unfiltered_sample_ct4, SEEK_SET)) { in calc_homozyg()
2656 if (fseeko(bedfile, bed_offset + (uint64_t)marker_uidx * unfiltered_sample_ct4, SEEK_SET)) { in calc_homozyg()
[all …]
H A Dplink_data.h29 int32_t make_bed(FILE* bedfile, uintptr_t bed_offset, char* bimname, char* outname, char* outname_e…
53 int32_t recode(uint32_t recode_modifier, FILE* bedfile, uintptr_t bed_offset, char* outname, char* …
H A Dplink.c323 FILE* bedfile = nullptr; in plink() local
542 bedfile = fopen(bedname, FOPEN_RB); in plink()
543 if (!bedfile) { in plink()
909 if (bedfile) { in plink()
910 if (fseeko(bedfile, 0, SEEK_END)) { in plink()
913 llxx = ftello(bedfile); in plink()
918 rewind(bedfile); in plink()
960 fclose(bedfile); in plink()
1292 if (bedfile && sample_ct) { in plink()
1434 if (bedfile) { in plink()
[all …]
H A Dplink_filter.c1413 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in load_oblig_missing()
1416 if (load_raw(unfiltered_sample_ct4, bedfile, loadbuf)) { in load_oblig_missing()
1643 if (fseeko(bedfile, bed_offset, SEEK_SET)) { in mind_filter()
1651 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in mind_filter()
1655 if (load_raw2(unfiltered_sample_ct4, unfiltered_sample_ctl2m1, final_mask, bedfile, loadbuf)) { in mind_filter()
2223 if (fseeko(bedfile, bed_offset, SEEK_SET)) { in calc_freqs_and_hwe()
2243 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in calc_freqs_and_hwe()
2247 if (load_raw(unfiltered_sample_ct4, bedfile, loadbuf)) { in calc_freqs_and_hwe()
2564 if (fseeko(bedfile, bed_offset, SEEK_SET)) { in write_missingness_reports()
2656 if (load_raw(unfiltered_sample_ct4, bedfile, loadbuf)) { in write_missingness_reports()
[all …]
H A Dplink_glm.c223 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in glm_scan_conditions()
227 if (load_raw(unfiltered_sample_ct4, bedfile, loadbuf_raw)) { in glm_scan_conditions()
4208 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in glm_linear_assoc_set_test()
4244 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in glm_linear_assoc_set_test()
4266 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in glm_linear_assoc_set_test()
5108 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in glm_linear_assoc()
5130 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in glm_linear_assoc()
5795 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in glm_logistic_assoc_set_test()
5817 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in glm_logistic_assoc_set_test()
6579 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in glm_logistic_assoc()
[all …]
H A Dplink_misc.c2509 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in write_stratified_freqs()
2527 if (load_raw(unfiltered_sample_ct4, bedfile, readbuf)) { in write_stratified_freqs()
2634 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in write_stratified_freqs()
2756 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in write_cc_freqs()
2769 if (load_raw(unfiltered_sample_ct4, bedfile, loadbuf)) { in write_cc_freqs()
2818 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in write_cc_freqs()
3084 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in sexcheck()
3090 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in sexcheck()
3149 if (fseeko(bedfile, bed_offset + ((uint64_t)marker_uidx) * unfiltered_sample_ct4, SEEK_SET)) { in sexcheck()
4091 if (load_raw(unfiltered_sample_ct4, bedfile, loadbuf)) { in fst_report()
[all …]
/dports/biology/py-crossmap/CrossMap-0.5.4/lib/cmmodule/
H A DannoGene.py7 def getCDSExonFromFile(bedfile): argument
11 for f in open(bedfile,'r'):
37 def getUTRExonFromFile(bedfile,utr=35): argument
43 for line in open(bedfile,'r'):
77 def getExonFromFile(bedfile): argument
81 for line in open(bedfile,'r'):
104 def getExonFromFile2(bedfile): argument
109 for line in open(bedfile,'r'):
/dports/biology/py-macs2/MACS-2.2.7.1/test/
H A Dtest_Parser.py11 self.bedfile = "test/tiny.bed.gz"
17 p = guess_parser( self.bedfile )
/dports/biology/py-bx-python/bx-python-0.8.13/scripts/
H A Dgene_fourfold_sites.py153 bedfile = args[1]
159 for chrom, strand, cds_exons, name in CDSReader(open(bedfile), format=format):
/dports/biology/py-pysam/pysam-0.18.0/samtools/
H A Dbam_ampliconclip.c629 static int bam_clip(samFile *in, samFile *out, samFile *reject, char *bedfile, in bam_clip() argument
643 if (load_bed_file_multi_ref(bedfile, param->use_strand, 1, bed_hash)) { in bam_clip()
951 char *bedfile = NULL, *fnout = "-"; in amplicon_clip_main() local
979 case 'b': bedfile = optarg; break; in amplicon_clip_main()
1003 if (!bedfile) { in amplicon_clip_main()
1055 ret = bam_clip(in, out, reject, bedfile, clipping, &param); in amplicon_clip_main()
H A Dbam_ampliconclip.c.pysam.c631 static int bam_clip(samFile *in, samFile *out, samFile *reject, char *bedfile, in bam_clip() argument
645 if (load_bed_file_multi_ref(bedfile, param->use_strand, 1, bed_hash)) { in bam_clip()
953 char *bedfile = NULL, *fnout = "-"; in amplicon_clip_main() local
981 case 'b': bedfile = optarg; break; in amplicon_clip_main()
1005 if (!bedfile) { in amplicon_clip_main()
1057 ret = bam_clip(in, out, reject, bedfile, clipping, &param); in amplicon_clip_main()
/dports/biology/samtools/samtools-1.14/
H A Dbam_ampliconclip.c629 static int bam_clip(samFile *in, samFile *out, samFile *reject, char *bedfile, in bam_clip() argument
643 if (load_bed_file_multi_ref(bedfile, param->use_strand, 1, bed_hash)) { in bam_clip()
951 char *bedfile = NULL, *fnout = "-"; in amplicon_clip_main() local
979 case 'b': bedfile = optarg; break; in amplicon_clip_main()
1003 if (!bedfile) { in amplicon_clip_main()
1055 ret = bam_clip(in, out, reject, bedfile, clipping, &param); in amplicon_clip_main()

12