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Searched refs:chrpos (Results 1 – 25 of 54) sorted by relevance

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/dports/biology/gmap/gmap-2020-09-12/src/
H A Doligoindex_hr.c9125 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()
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H A Dget-genome.c294 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()
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H A Diit_get.c359 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++;
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H A Dchrnum.c72 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()
H A Dknownsplicing.c251 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()
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H A Dcigar.c2038 *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()
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H A Dmatch.c77 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()
H A Dcigar.h29 int *nindels, bool *plusp, Chrnum_T *chrnum, Chrpos_T *chrpos,
38 int *nindels, bool *plusp, Chrnum_T *chrnum, Chrpos_T *chrpos,
H A Dindexdb-write.c296 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()
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H A Dsamread.c535 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) {
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H A Dsplicetrie_build.c389 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()
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H A Dparserange.c250 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()
/dports/biology/gmap/gmap-2020-09-12/util/
H A Dfa_coords.pl.in330 $string .= sprintf("%d..%d",$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});
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H A Dvcf_iit.pl.in14 $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…
H A Dgvf_iit.pl.in13 $chrpos = $fields[3]; # GVF file is 1-based
48 print ">$rsid $chr:$chrpos $snp_type $snp_strand\n";
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/bem/src/
H A DTABIPBWrap.c33 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()
H A Dmain.c120 …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()
H A Dtabipb_sph.pyx76 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)
H A Dtabipb.c137 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()
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/dports/comms/wsjtz/wsjtx/lib/
H A Doptions.f90107 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
/dports/biology/kallisto/kallisto-0.46.1/src/
H A DGeneModel.h33 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));
H A DGeneModel.cpp41 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()
/dports/databases/couchdb3/apache-couchdb-3.2.1/src/jiffy/c_src/
H A Ddecoder.c201 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()
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/dports/dns/yadifa/yadifa-2.5.3-10333/lib/dnsdb/src/
H A Dzdb_zone_write_text.c141 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()
/dports/textproc/sablotron/Sablot-1.0.3/src/command/
H A Dsabcmd.cpp212 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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