/dports/biology/plink/plink-ng-79b2df8c/1.9/ |
H A D | plink_ld.h | 132 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 …]
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H A D | plink_assoc.h | 32 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…
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H A D | plink_calc.h | 58 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…
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H A D | plink_family.h | 74 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, …
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H A D | plink_lasso.c | 119 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 …]
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H A D | plink_misc.h | 88 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…
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H A D | plink_glm.h | 31 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, …
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H A D | plink_lasso.h | 21 …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…
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H A D | plink_filter.h | 57 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…
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H A D | plink_rserve.h | 21 …ugin_host_or_socket, int32_t rplugin_port, uint32_t rplugin_debug, FILE* bedfile, uintptr_t bed_of…
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H A D | plink_ld.c | 980 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 …]
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H A D | plink_rserve.c | 33 …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()
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H A D | plink_homozyg.h | 44 int32_t calc_homozyg(Homozyg_info* hp, FILE* bedfile, uintptr_t bed_offset, uint32_t marker_ct, uin…
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H A D | plink_homozyg.c | 877 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 …]
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H A D | plink_data.h | 29 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* …
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H A D | plink.c | 323 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 …]
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H A D | plink_filter.c | 1413 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 …]
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H A D | plink_glm.c | 223 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 …]
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H A D | plink_misc.c | 2509 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 …]
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/dports/biology/py-crossmap/CrossMap-0.5.4/lib/cmmodule/ |
H A D | annoGene.py | 7 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'):
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/dports/biology/py-macs2/MACS-2.2.7.1/test/ |
H A D | test_Parser.py | 11 self.bedfile = "test/tiny.bed.gz" 17 p = guess_parser( self.bedfile )
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/dports/biology/py-bx-python/bx-python-0.8.13/scripts/ |
H A D | gene_fourfold_sites.py | 153 bedfile = args[1] 159 for chrom, strand, cds_exons, name in CDSReader(open(bedfile), format=format):
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/dports/biology/py-pysam/pysam-0.18.0/samtools/ |
H A D | bam_ampliconclip.c | 629 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, ¶m); in amplicon_clip_main()
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H A D | bam_ampliconclip.c.pysam.c | 631 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, ¶m); in amplicon_clip_main()
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/dports/biology/samtools/samtools-1.14/ |
H A D | bam_ampliconclip.c | 629 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, ¶m); in amplicon_clip_main()
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