/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | oligoindex_hr.c | 9125 chrpos--; in store_9mers_fwd_partial() 9136 chrpos--; in store_9mers_fwd_partial() 9148 chrpos--; in store_9mers_fwd_partial() 9159 chrpos--; in store_9mers_fwd_partial() 9229 chrpos--; in store_8mers_fwd_partial() 9240 chrpos--; in store_8mers_fwd_partial() 9252 chrpos--; in store_8mers_fwd_partial() 9263 chrpos--; in store_8mers_fwd_partial() 9333 chrpos--; in store_7mers_fwd_partial() 9344 chrpos--; in store_7mers_fwd_partial() [all …]
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H A D | get-genome.c | 294 printf("%s\t%u\t%u\tA/C\n",chromosome1,chrpos,chrpos); in print_sequence() 295 printf("%s\t%u\t%u\tA/G\n",chromosome1,chrpos,chrpos); in print_sequence() 296 printf("%s\t%u\t%u\tA/T\n",chromosome1,chrpos,chrpos); in print_sequence() 299 printf("%s\t%u\t%u\tC/A\n",chromosome1,chrpos,chrpos); in print_sequence() 300 printf("%s\t%u\t%u\tC/G\n",chromosome1,chrpos,chrpos); in print_sequence() 301 printf("%s\t%u\t%u\tC/T\n",chromosome1,chrpos,chrpos); in print_sequence() 304 printf("%s\t%u\t%u\tG/A\n",chromosome1,chrpos,chrpos); in print_sequence() 305 printf("%s\t%u\t%u\tG/C\n",chromosome1,chrpos,chrpos); in print_sequence() 306 printf("%s\t%u\t%u\tG/T\n",chromosome1,chrpos,chrpos); in print_sequence() 309 printf("%s\t%u\t%u\tT/A\n",chromosome1,chrpos,chrpos); in print_sequence() [all …]
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H A D | iit_get.c | 359 chrpos++; in print_interval_tally() 362 while (chrpos <= intervalend && chrpos <= coordend) { in print_interval_tally() 381 chrpos++; in print_interval_tally() 419 chrpos++; in print_interval_runlength() 422 while (chrpos <= intervalend && chrpos <= coordend) { in print_interval_runlength() 424 chrpos++; in print_interval_runlength() 466 chrpos++; in compute_totals_tally() 469 while (chrpos <= intervalend && chrpos <= coordend) { in compute_totals_tally() 473 chrpos++; in compute_totals_tally() 512 chrpos++; [all …]
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H A D | chrnum.c | 72 Chrpos_T chrpos; in Chrnum_print_position() local 79 chrpos = position; in Chrnum_print_position() 82 chrpos = position - Univinterval_low(Univ_IIT_interval(chromosome_iit,index)); in Chrnum_print_position() 86 printf("#%d (chr%s):%u ",chrnum,label,chrpos); in Chrnum_print_position()
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H A D | knownsplicing.c | 251 Chrpos_T chrlength, chrpos; in Knownsplicing_retrieve_via_splicesites() local 307 chrpos = Interval_low(interval); in Knownsplicing_retrieve_via_splicesites() 308 position = chrpos + chroffset; in Knownsplicing_retrieve_via_splicesites() 313 chr,chrpos,chrlength); in Knownsplicing_retrieve_via_splicesites() 414 chrpos = Interval_low(interval); in Knownsplicing_retrieve_via_splicesites() 415 position = chrpos + chroffset; in Knownsplicing_retrieve_via_splicesites() 422 chr,chrpos,chrlength); in Knownsplicing_retrieve_via_splicesites() 453 chr,chrpos); in Knownsplicing_retrieve_via_splicesites() 487 chr,chrpos); in Knownsplicing_retrieve_via_splicesites() 522 chr,chrpos); in Knownsplicing_retrieve_via_splicesites() [all …]
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H A D | cigar.c | 2038 *chrpos = 0; in Cigar_compute_main() 2107 *chrpos = 0; in Cigar_compute_main() 2141 *chrpos = 0; in Cigar_compute_main() 2150 if (*chrpos > Substring_chrlength(substring)) { in Cigar_compute_main() 2151 *chrpos -= Substring_chrlength(substring); in Cigar_compute_main() 2166 *chrpos = 0; in Cigar_compute_main() 2175 *chrpos -= Substring_chrlength(substring); in Cigar_compute_main() 2309 *chrpos = 0; in Cigar_compute_supplemental() 2318 *chrpos -= Substring_chrlength(substring); in Cigar_compute_supplemental() 2333 *chrpos = 0; in Cigar_compute_supplemental() [all …]
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H A D | match.c | 77 return this->chrpos; in Match_chrpos() 147 new->chrpos = position; in Match_new() 150 new->chrpos = position - Univinterval_low(Univ_IIT_interval(chromosome_iit,index)); in Match_new() 218 this->querypos,this->chrnum,chr,this->chrpos,this->forwardp, in Match_print()
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H A D | cigar.h | 29 int *nindels, bool *plusp, Chrnum_T *chrnum, Chrpos_T *chrpos, 38 int *nindels, bool *plusp, Chrnum_T *chrnum, Chrpos_T *chrpos,
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H A D | indexdb-write.c | 296 Chrpos_T chrpos = 0U; in Indexdb_count_offsets() local 450 chrpos = 0U; in Indexdb_count_offsets() 486 Chrpos_T chrpos = 0U; in Indexdb_write_offsets() local 739 chrpos = 0U; in Indexdb_write_offsets() 829 Chrpos_T chrpos = 0U; in Indexdb_write_offsets_huge() local 1115 chrpos = 0U; in Indexdb_write_offsets_huge() 1396 Chrpos_T chrpos = 0U; 1594 chrpos = 0U; 1889 chrpos = 0U; 2158 chrpos = 0U; in compute_positions() [all …]
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H A D | samread.c | 535 Chrpos_T chrpos, mate_chrpos; in Samread_parse_acc_and_softclip_fromfile() local 579 if (sscanf(substring,"%u",&chrpos) != 1) { in Samread_parse_acc_and_softclip_fromfile() 583 *genomicpos += chrpos; in Samread_parse_acc_and_softclip_fromfile() 725 if (sscanf(p,"%u",&(*chrpos)) != 1) { 729 debug(printf(" chrpos = %u\n",*chrpos)); 895 debug(printf(" chrpos = %u\n",*chrpos)); 990 Chrpos_T chrpos; in Samread_parse_genomicpos_fromfile() local 1031 if (sscanf(substring,"%u",&chrpos) != 1) { in Samread_parse_genomicpos_fromfile() 1035 genomicpos += chrpos; in Samread_parse_genomicpos_fromfile() 1433 if (sscanf(p,"%u",&(*chrpos)) != 1) { [all …]
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H A D | splicetrie_build.c | 389 Chrpos_T chrlength, chrpos; in Splicetrie_retrieve_via_splicesites() local 455 chr,chrpos,chrlength); in Splicetrie_retrieve_via_splicesites() 578 chr,chrpos,chrlength); in Splicetrie_retrieve_via_splicesites() 612 chr,chrpos); in Splicetrie_retrieve_via_splicesites() 653 chr,chrpos); in Splicetrie_retrieve_via_splicesites() 695 chr,chrpos); in Splicetrie_retrieve_via_splicesites() 735 chr,chrpos); in Splicetrie_retrieve_via_splicesites() 995 chr,chrpos); in Splicetrie_retrieve_via_introns() 1035 chr,chrpos); in Splicetrie_retrieve_via_introns() 1094 chr,chrpos); in Splicetrie_retrieve_via_introns() [all …]
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H A D | parserange.c | 250 convert_to_chrpos (Chrpos_T *chrpos, char *genomesubdir, char *fileroot, Univcoord_T position) { in convert_to_chrpos() argument 264 chromosome = Univ_IIT_string_from_position(&(*chrpos),position-1,chromosome_iit); in convert_to_chrpos() 265 *chrpos += 1U; /* Bring back to 1-based */ in convert_to_chrpos() 273 convert_to_chrpos_iit (Chrpos_T *chrpos, Univ_IIT_T chromosome_iit, Univcoord_T position) { in convert_to_chrpos_iit() argument 277 chromosome = Univ_IIT_string_from_position(&(*chrpos),position-1,chromosome_iit); in convert_to_chrpos_iit() 278 *chrpos += 1U; /* Bring back to 1-based */ in convert_to_chrpos_iit()
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/dports/biology/gmap/gmap-2020-09-12/util/ |
H A D | fa_coords.pl.in | 330 $string .= sprintf("%d..%d",$chrpos{$chr}+$seglength-1,$chrpos{$chr}); 332 $string .= sprintf("%d..%d",$chrpos{$chr}+$seglength-1,$chrpos{$chr}); 334 $string .= sprintf("%d..%d",$chrpos{$chr},$chrpos{$chr}+$seglength-1); 392 $chrpos{$chr} = $2; 419 $chrpos{$chr} = $1; 519 $string .= sprintf("%d..%d",$chrpos{$chr}+$seglength-1,$chrpos{$chr}); 521 $string .= sprintf("%d..%d",$chrpos{$chr}+$seglength-1,$chrpos{$chr}); 523 $string .= sprintf("%d..%d",$chrpos{$chr},$chrpos{$chr}+$seglength-1); 604 $string .= sprintf("%d..%d",$chrpos{$chr}+$seglength-1,$chrpos{$chr}); 606 $string .= sprintf("%d..%d",$chrpos{$chr}+$seglength-1,$chrpos{$chr}); [all …]
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H A D | vcf_iit.pl.in | 14 $chrpos = $fields[1]; 36 print ">$id $chr:$chrpos "; 40 print ">$id $chr:$chrpos "; 44 …print STDERR "Ref allele $ref_allele and alt allele $alt_allele for $id at $chr:$chrpos are the sa…
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H A D | gvf_iit.pl.in | 13 $chrpos = $fields[3]; # GVF file is 1-based 48 print ">$rsid $chr:$chrpos $snp_type $snp_strand\n";
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/bem/src/ |
H A D | TABIPBWrap.c | 33 fprintf(wfp, "%f %f %f %f\n", vars->chrpos[3*i], vars->chrpos[3*i + 1], in apbs2tabipb_() 34 vars->chrpos[3*i + 2], vars->atmrad[i]); in apbs2tabipb_() 59 fprintf(wfp, "%f %f %f %f\n", vars->chrpos[3*i], vars->chrpos[3*i + 1], in sphinx2tabipb() 60 vars->chrpos[3*i + 2], vars->atmrad[i]); in sphinx2tabipb()
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H A D | main.c | 120 …if ((main_vars->chrpos = (double *) calloc(3 * main_parm->number_of_lines, sizeof(double))) == NUL… in main() 133 main_vars->chrpos[3*i] = a1; in main() 134 main_vars->chrpos[3*i + 1] = a2; in main() 135 main_vars->chrpos[3*i + 2] = a3; in main() 150 free(main_vars->chrpos); in main()
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H A D | tabipb_sph.pyx | 76 tabipbvars.chrpos = <double*> malloc(3 * natm * sizeof(double)); 81 tabipbvars.chrpos[i*3] = atom['pos'][0] 82 tabipbvars.chrpos[i*3+1] = atom['pos'][1] 83 tabipbvars.chrpos[i*3+2] = atom['pos'][2] 89 free(tabipbvars.chrpos)
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H A D | tabipb.c | 137 r[0] = vars->chrpos[3*i]; in tabipb() 138 r[1] = vars->chrpos[3*i+1]; in tabipb() 139 r[2] = vars->chrpos[3*i+2]; in tabipb() 141 diff[0] = r[0] - vars->chrpos[3*j]; in tabipb() 142 diff[1] = r[1] - vars->chrpos[3*j+1]; in tabipb() 143 diff[2] = r[2] - vars->chrpos[3*j+2]; in tabipb() 218 r_s[0] = vars->chrpos[3*j] - tr_xyz[3*i]; in comp_source() 219 r_s[1] = vars->chrpos[3*j + 1] - tr_xyz[3*i + 1]; in comp_source() 277 s[0] = vars->chrpos[3*i]; in comp_pot() 278 s[1] = vars->chrpos[3*i + 1]; in comp_pot() [all …]
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/dports/comms/wsjtz/wsjtx/lib/ |
H A D | options.f90 | 107 integer :: chrpos, length, st, id = 0 local 186 chrpos = scan(options, chr) 188 chrpos = 0 192 if (chrpos == 0) then 198 if (chrpos < len_trim(options)) then 199 if (options(chrpos+1:chrpos+1) == ':') then
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/dports/biology/kallisto/kallisto-0.46.1/src/ |
H A D | GeneModel.h | 33 int chrpos; // 0-based position of left-most bp member 37 TranscriptAlignment() : chr(-1), chrpos(-1), strand(true) {} in TranscriptAlignment() 40 …bool comparison = (chr == o.chr) && (chrpos == o.chrpos) && (strand == o.strand) && (cigar.size() … 55 uint32_t value = std::hash<int>()((x.chr+1)*x.chrpos + ((int) x.strand));
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H A D | GeneModel.cpp | 41 aln.chrpos = -1; in translateTrPosition() 57 aln.chrpos = model.start; in translateTrPosition() 64 aln.chrpos = exon.start + trpos; // left-most position in translateTrPosition() 95 aln.chrpos = model.start; in translateTrPosition() 102 aln.chrpos = exon.start + trpos; in translateTrPosition()
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/dports/databases/couchdb3/apache-couchdb-3.2.1/src/jiffy/c_src/ |
H A D | decoder.c | 201 int chrpos; in dec_string() local 309 chrpos = 0; in dec_string() 313 chrbuf[chrpos++] = d->p[ui++]; in dec_string() 321 chrbuf[chrpos++] = d->p[ui]; in dec_string() 325 chrbuf[chrpos++] = '\b'; in dec_string() 329 chrbuf[chrpos++] = '\f'; in dec_string() 333 chrbuf[chrpos++] = '\n'; in dec_string() 337 chrbuf[chrpos++] = '\r'; in dec_string() 341 chrbuf[chrpos++] = '\t'; in dec_string() 360 hi = unicode_to_utf8(hi, (unsigned char*) chrbuf+chrpos); in dec_string() [all …]
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/dports/dns/yadifa/yadifa-2.5.3-10333/lib/dnsdb/src/ |
H A D | zdb_zone_write_text.c | 141 char *chrpos = rawmemchr(str, '@'); in zdb_zone_write_text_fqdn_print() local 142 if(chrpos == str_limit) // not found in zdb_zone_write_text_fqdn_print() 145 chrpos = rawmemchr(str, '$'); in zdb_zone_write_text_fqdn_print() 147 if(chrpos == str_limit) // not found in zdb_zone_write_text_fqdn_print() 163 char *chrpos = memchr(str, '@', len); in zdb_zone_write_text_fqdn_print() 164 if(chrpos == NULL) // not found in zdb_zone_write_text_fqdn_print() 166 chrpos = memchr(str, '$', len); in zdb_zone_write_text_fqdn_print() 168 if(chrpos == NULL) // not found in zdb_zone_write_text_fqdn_print()
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/dports/textproc/sablotron/Sablot-1.0.3/src/command/ |
H A D | sabcmd.cpp | 212 int chrpos(const char *text, char c) in chrpos() function 259 int eqpos = chrpos(stripped, '='); in findSwitch() 287 int eqpos = chrpos(text, '='); in applySwitch() 347 if (((chrpos(argv[i], '=')) != -1) && (argv[i][0] != BARE_SIGN)) in readSwitches() 377 pos = chrpos(array[i], '='); in xformToPairs()
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