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Searched refs:chrend (Results 1 – 19 of 19) sorted by relevance

/dports/biology/gmap/gmap-2020-09-12/src/
H A Dstage2.h52 Chrpos_T chrstart, Chrpos_T chrend,
59 Chrpos_T chrstart, Chrpos_T chrend,
72 Chrpos_T chrstart, Chrpos_T chrend,
81 Chrpos_T chrstart, Chrpos_T chrend,
90 Chrpos_T chrstart, Chrpos_T chrend,
H A Dparserange.h26 Chrpos_T *chrstart, Chrpos_T *chrend,
33 Chrpos_T *chrstart, Chrpos_T *chrend,
38 Parserange_simple (char **div, bool *revcomp, Chrpos_T *chrstart, Chrpos_T *chrend,
H A Dgregion.c65 Chrpos_T chrend; member
140 return this->chroffset + this->chrend; in Gregion_genomicend()
150 return this->chrend; in Gregion_chrend()
270 new->chrend = new->chrstart + new->genomiclength; in Gregion_new()
282 new->extentend = new->chrend + (querylength - queryend); in Gregion_new()
290 new->extentend = new->chrend + querystart; in Gregion_new()
451 x_genomicend = x->chroffset + x->chrend; in gregion_overlap_p()
453 y_genomicend = y->chroffset + y->chrend; in gregion_overlap_p()
926 this->chrend = this->chrlength - 1; in Gregion_extend()
928 this->chrend += right; in Gregion_extend()
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H A Ddiag.h51 Chrpos_T chrstart, Chrpos_T chrend,
55 int querylength, Chrpos_T chrstart, Chrpos_T chrend,
H A Dparserange.c372 Chrpos_T *chrstart, Chrpos_T *chrend, in Parserange_universal() argument
430 *chrend = *chrstart + *genomiclength; in Parserange_universal()
518 *chrend = *chrstart + *genomiclength; in Parserange_universal()
546 Chrpos_T *chrstart, Chrpos_T *chrend, in Parserange_universal_iit() argument
595 *chrend = *chrstart + *genomiclength; in Parserange_universal_iit()
663 *chrend = *chrstart + *genomiclength; in Parserange_universal_iit()
682 Parserange_simple (char **div, bool *revcomp, Chrpos_T *chrstart, Chrpos_T *chrend, in Parserange_simple() argument
727 *chrend = *chrstart + length; in Parserange_simple()
H A Dget-genome.c918 Chrpos_T genomiclength, chrlength, chrstart, chrend; in main() local
1594 divstring2 = Univ_IIT_string_from_position(&chrend,genomicstart+genomiclength-1U,chromosome_iit); in main()
1600 chrend += 1U; in main()
1601 debug(printf("Query translated to %s:%u..%u\n",divstring,chrstart,chrend)); in main()
1610 matches = get_matches(&nmatches,&sign,divstring,chrstart,chrend,revcomp, in main()
1617 if (codingp == false || IIT_gene_overlapp(map_iit,leftflanks[i],chrstart,chrend) == true) { in main()
1627 if (codingp == false || IIT_gene_overlapp(map_iit,matches[i],chrstart,chrend) == true) { in main()
1787 Parserange_universal_iit(&segment,&revcomp,&genomicstart,&genomiclength,&chrstart,&chrend, in main()
1798 chrend += 1U; in main()
1799 debug(printf("Query translated to %s:%u..%u\n",divstring,chrstart,chrend)); in main()
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H A Dstage2.c5827 Chrpos_T chrstart, Chrpos_T chrend, in Stage2_scan() argument
5890 /*chrpos*/(chrhigh-chroffset)-chrend); in Stage2_scan()
6548 Chrpos_T chrstart, Chrpos_T chrend, in Stage2_compute() argument
6654 mappingend = chroffset + chrend; in Stage2_compute()
6657 mappingend = chroffset + chrend + 1; in Stage2_compute()
6658 chrpos = (chrhigh - chroffset) - chrend; in Stage2_compute()
6703 /*chrpos*/(chrhigh-chroffset)-chrend); in Stage2_compute()
7070 Chrpos_T chrstart, Chrpos_T chrend, in Stage2_compute_one() argument
7127 /*chrpos*/(chrhigh-chroffset)-chrend); in Stage2_compute_one()
7241 Chrpos_T chrstart, Chrpos_T chrend, in Stage2_compute_starts() argument
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H A Ddiag.c595 Chrpos_T chrstart, Chrpos_T chrend, in Diag_compute_bounds() argument
607 genomiclength = chrend - chrstart; in Diag_compute_bounds()
611 chrterm = chrend; in Diag_compute_bounds()
613 chrinit = (chrhigh - chroffset) - chrend; in Diag_compute_bounds()
902 int querylength, Chrpos_T chrstart, Chrpos_T chrend, in Diag_max_bounds() argument
909 chrterm = chrend; in Diag_max_bounds()
911 chrinit = (chrhigh - chroffset) - chrend; in Diag_max_bounds()
H A Doligoindex_hr.h132 Chrpos_T chrstart, Chrpos_T chrend,
H A Diit-read-univ.c266 Chrpos_T genomiclength, chrstart, chrend, chrlength; in Univ_IIT_altlocp() local
308 &chrstart,&chrend,&chroffset,&chrlength, in Univ_IIT_altlocp()
979 Chrpos_T chrstart, chrend; in Univ_IIT_dump_contigs() local
996 chrend = endpos - chroffset; in Univ_IIT_dump_contigs()
1002 printf("%s:%u..%u\t",chrstring,chrstart+1U,chrend+1U); in Univ_IIT_dump_contigs()
1008 printf("%s:%u..%u\t",chrstring,chrend+1U,chrstart+1U); in Univ_IIT_dump_contigs()
1011 printf("%s:%u..%u\t",chrstring,chrstart+1U,chrend+1U); in Univ_IIT_dump_contigs()
H A Dkmer-search.c4899 Chrpos_T chrstart, chrend; in Kmer_remap_transcriptome() local
5033 assert(chrstart < chrend); in Kmer_remap_transcriptome()
5035 chrstart,chrend,lowbound,highbound)); in Kmer_remap_transcriptome()
5036 if (chrstart <= highbound && chrend >= lowbound) { in Kmer_remap_transcriptome()
5044 assert(chrend < chrstart); in Kmer_remap_transcriptome()
5046 chrend,chrstart,lowbound,highbound)); in Kmer_remap_transcriptome()
5128 chrend = exonstarts[exoni] - exonpos; /* gminus */ in Kmer_remap_transcriptome()
5142 assert(chrend < chrstart); in Kmer_remap_transcriptome()
5144 chrend,chrstart,lowbound,highbound)); in Kmer_remap_transcriptome()
5152 assert(chrstart < chrend); in Kmer_remap_transcriptome()
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H A Dstage3.c11103 Chrpos_T chrstart, chrend; in traverse_dual_break() local
11356 chrend = genomedp3; in traverse_dual_break()
11365 chrstart,chrend,watsonp)); in traverse_dual_break()
13900 Chrpos_T chrstart, chrend; in path_compute_end5()
14047 Chrpos_T chrstart, chrend; in path_compute_end3()
15988 chrstart,chrend, in Stage3_compute_ends()
16073 chrend = start->genomepos; in Stage3_compute_ends()
16095 chrstart,chrend, in Stage3_compute_ends()
16211 chrstart,chrend, in Stage3_compute_ends()
16288 chrend = start->genomepos; in Stage3_compute_ends()
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H A Dgmap.c1152 Chrpos_T chrstart, Chrpos_T chrend, bool watsonp, int genestrand, in update_stage3middle_list() argument
1206 chrstart,chrend,Sequence_subseq_offset(queryseq))); in update_stage3middle_list()
1209 chrstart,chrend,chroffset,chrhigh,/*plusp*/watsonp,genestrand, in update_stage3middle_list()
1256 Chrpos_T chrstart, Chrpos_T chrend, bool watsonp, int genestrand, in update_stage3list() argument
1320 chrstart,chrend,Sequence_subseq_offset(queryseq))); in update_stage3list()
1980 Chrpos_T *chrstart, Chrpos_T *chrend, in middle_piece_local_p() argument
2030 *chrend = Stage3_chrstart(to); in middle_piece_local_p()
2050 *chrend = Stage3_chrend(from); in middle_piece_local_p()
3633 Chrpos_T chrstart, chrend, chrlength; in check_middle_piece_local() local
3699 querystart,queryend,chrstart,chrend)); in check_middle_piece_local()
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H A Doligoindex_hr.c34144 int querystart, int queryend, int querylength, Chrpos_T chrstart, Chrpos_T chrend, in Oligoindex_get_mappings() argument
34173 if (chrend <= chrstart) { in Oligoindex_get_mappings()
34181 genomiclength = chrend - chrstart; in Oligoindex_get_mappings()
34185 chrinit = (chrhigh - chroffset) - chrend; in Oligoindex_get_mappings()
/dports/biology/gmap/gmap-2020-09-12/util/
H A Dgmap_process.pl.in119 ($chrstart,$chrend) = $coords{$contig} =~ /\S+:(\d+)\.\.(\d+)/;
121 $universal_coord += $chrend - $chrstart + 1;
124 $universal_coord += $chrend - $chrstart + 1;
125 $universal_coord += $chrend - $chrstart + 1;
128 $universal_coord += $chrend - $chrstart + 1;
132 $universal_coord += $chrend - $chrstart + 1;
H A Dmd_coords.pl.in135 my %chrend = (); # Need to reset, in case this procedure is run again
172 if (!defined($chrend{$chr})) {
173 $chrend{$chr} = 0;
175 $chrstart = $chrend{$chr} + 1;
176 $chrend = $chrend{$chr} + $seglength;
177 $chrend{$chr} = $chrend;
181 $chrend = $fields[$chrendcol-1];
184 $chrinfo = "$chr:$chrstart..$chrend";
186 $chrinfo = "$chr:$chrend..$chrstart";
189 $chrinfo = "$chr:$chrstart..$chrend";
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/dports/textproc/p5-Text-ExtractWords/Text-ExtractWords-0.08/
H A DExtractWords.xs30 char chrend[] = " ,;.:\x0A\x0D\x09\"'?!+-*/()[]"; variable
73 } else if(x > 0 && isDIGIT(s[y-1]) && strchr(chrend, s[y+1])) { in unescape_str()
76 if(!strchr(chrend, s[x-j])) s[x] = ' '; in unescape_str()
/dports/shells/zsh/zsh-5.8.1/Src/
H A Dpattern.c2680 char *start, *save, *chrop, *chrend, *compend; in patmatch() local
2726 chrend = exactend; in patmatch()
2729 chrend = chrop + P_LS_LEN(scan); in patmatch()
2732 while (chrop < chrend && patinput < patinend) { in patmatch()
2748 patint_t chpa = CHARREFINC(chrop, chrend, &badpa); in patmatch()
2756 if (chrop < chrend) { in patmatch()
2758 exactend = chrend; in patmatch()
/dports/biology/gmap/gmap-2020-09-12/
H A DChangeLog2372 * stage3.c, stage3.h: Limiting chrend for Stage2_compute_starts and
2384 removed the check on chrend going past chrhigh. The truncated coordinates
2385 can cause chrend to be less than chrstart if the alignment straddles a
2451 * stage3.c: Fixed computation of chrstart and chrend before final
7962 * gregion.c: In Gregion_extend, when chrend goes past chrhigh, setting it to
8363 * gregion.c: For determining overlaps, using chrstart and chrend instead of
9935 * stage3.c: Fixed bug in computing chrstart and chrend for
12817 * stage3.h: Providing accessor commands for chrnum, chrstart, and chrend
16258 calculation of chrend in finding right bound for short-end splicing.