/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | stage2.h | 52 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,
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H A D | parserange.h | 26 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,
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H A D | gregion.c | 65 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() [all …]
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H A D | diag.h | 51 Chrpos_T chrstart, Chrpos_T chrend, 55 int querylength, Chrpos_T chrstart, Chrpos_T chrend,
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H A D | parserange.c | 372 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()
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H A D | get-genome.c | 918 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() [all …]
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H A D | stage2.c | 5827 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 [all …]
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H A D | diag.c | 595 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()
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H A D | oligoindex_hr.h | 132 Chrpos_T chrstart, Chrpos_T chrend,
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H A D | iit-read-univ.c | 266 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()
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H A D | kmer-search.c | 4899 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() [all …]
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H A D | stage3.c | 11103 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() [all …]
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H A D | gmap.c | 1152 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() [all …]
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H A D | oligoindex_hr.c | 34144 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()
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/dports/biology/gmap/gmap-2020-09-12/util/ |
H A D | gmap_process.pl.in | 119 ($chrstart,$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 - $chrstart + 1;
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H A D | md_coords.pl.in | 135 my %chrend = (); # Need to reset, in case this procedure is run again 172 if (!defined($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"; [all …]
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/dports/textproc/p5-Text-ExtractWords/Text-ExtractWords-0.08/ |
H A D | ExtractWords.xs | 30 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()
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/dports/shells/zsh/zsh-5.8.1/Src/ |
H A D | pattern.c | 2680 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()
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/dports/biology/gmap/gmap-2020-09-12/ |
H A D | ChangeLog | 2372 * 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.
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