/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | junction.c | 373 static char complCode[128] = COMPLEMENT_LC; variable 381 temp = complCode[(int) sequence[i]]; in make_complement_inplace() 382 sequence[i] = complCode[(int) sequence[j]]; in make_complement_inplace() 386 sequence[i] = complCode[(int) sequence[i]]; in make_complement_inplace()
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H A D | filestring.c | 322 static char complCode[128] = COMPLEMENT_LC; variable 333 temp = complCode[(int) *p]; in revcomp_inplace() 334 *p++ = complCode[(int) *q]; in revcomp_inplace() 338 *p = complCode[(int) *p]; in revcomp_inplace()
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H A D | boyer-moore.c | 356 static char complCode[128] = COMPLEMENT_LC; 384 *g_alt = complCode[(int) c2_alt]; 385 return complCode[(int) c2];
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H A D | mdprint.c | 23 static char complCode[128] = COMPLEMENT_LC; variable 31 complement[j] = complCode[(int) sequence[i]]; in make_complement_buffered()
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H A D | sequence.c | 1014 static char complCode[128] = COMPLEMENT_LC; variable 1023 complement[j] = complCode[(int) sequence[i]]; in make_complement() 1056 complement[j] = uppercaseCode[(int) complCode[(int) sequence[i]]]; 1071 complement[j] = complCode[(int) sequence[i]]; 1085 temp = complCode[(int) sequence[i]]; in make_complement_inplace() 1086 sequence[i] = complCode[(int) sequence[j]]; in make_complement_inplace() 1090 sequence[i] = complCode[(int) sequence[i]]; in make_complement_inplace()
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H A D | simplepair.c | 1137 static char complCode[128] = COMPLEMENT_LC; variable 1286 sprintf(token,"%c",tolower(complCode[(int) this->genome])); in compute_md_string() 1289 sprintf(token,"%c",complCode[(int) this->genome]); in compute_md_string() 1336 sprintf(token,"%c",complCode[(int) this->genome]); in compute_md_string() 1390 PUTC(complCode[(int) contents[i]],fp); in print_chopped_revcomp() 1421 PUTC(complCode[(int) contents[i]],fp); in print_chopped_end_revcomp() 1427 PUTC(complCode[(int) contents[i]],fp); in print_chopped_end_revcomp()
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H A D | pair.c | 820 static char complCode[128] = COMPLEMENT_LC; variable 2080 temp = complCode[(int) sequence[i]]; in make_complement_inplace() 4669 *g_alt = complCode[(int) c2_alt]; 4670 return complCode[(int) c2]; 4830 PUTC(complCode[(int) contents[i]],fp); in print_chopped_revcomp() 4861 PUTC(complCode[(int) contents[i]],fp); in print_chopped_end_revcomp() 4867 PUTC(complCode[(int) contents[i]],fp); in print_chopped_end_revcomp() 8561 donor[0] = complCode[(int) acceptor[1]]; 8562 acceptor[1] = complCode[(int) temp]; 8565 donor[1] = complCode[(int) acceptor[0]]; [all …]
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H A D | chimera.c | 635 static char *complCode = COMPLEMENT_UC; variable 781 *donor1 = complCode[(int) Genome_get_char(genome,left-1)]; in Chimera_find_breakpoint() 782 *donor2 = complCode[(int) Genome_get_char(genome,left-2)]; in Chimera_find_breakpoint() 801 *acceptor2 = complCode[(int) Genome_get_char(genome,left+2)]; in Chimera_find_breakpoint() 802 *acceptor1 = complCode[(int) Genome_get_char(genome,left+1)]; in Chimera_find_breakpoint()
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H A D | pairpool.c | 1014 static char complCode[128] = COMPLEMENT_LC; variable 1076 debug8(printf("At %u, genomicnt is %c\n",genomicpos,complCode[(int) c2])); in get_genomic_nt() 1077 *g_alt = complCode[(int) c2_alt]; in get_genomic_nt() 1078 return complCode[(int) c2]; in get_genomic_nt()
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H A D | get-genome.c | 544 static char complCode[128] = COMPLEMENT_LC; variable 552 complement[j] = complCode[(int) sequence[i]]; 565 temp = complCode[(int) sequence[i]]; in make_complement_inplace() 566 sequence[i] = complCode[(int) sequence[j]]; in make_complement_inplace() 570 sequence[i] = complCode[(int) sequence[i]]; in make_complement_inplace()
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H A D | dynprog_cdna.c | 68 static char complCode[128] = COMPLEMENT_LC; variable 130 debug8(printf("At %u, genomicnt is %c\n",genomicpos,complCode[(int) c2])); in get_genomic_nt() 131 *g_alt = complCode[(int) c2_alt]; in get_genomic_nt() 132 return complCode[(int) c2]; in get_genomic_nt()
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H A D | dynprog_single.c | 105 static char complCode[128] = COMPLEMENT_LC; variable 167 debug8(printf("At %u, genomicnt is %c\n",genomicpos,complCode[(int) c2])); in get_genomic_nt() 168 *g_alt = complCode[(int) c2_alt]; in get_genomic_nt() 169 return complCode[(int) c2]; in get_genomic_nt()
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H A D | sam_sort.c | 216 static char complCode[128] = COMPLEMENT_LC; variable 224 temp = complCode[(int) sequence[i]]; in make_complement_inplace() 225 sequence[i] = complCode[(int) sequence[j]]; in make_complement_inplace() 229 sequence[i] = complCode[(int) sequence[i]]; in make_complement_inplace()
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H A D | iit_get.c | 167 static char complCode[128] = COMPLEMENT_LC; variable 184 printf("%c",complCode[(int) sequence[i]]); in print_complement() 237 printf("[%c]",complCode[(int) centerchar]); in print_interval_centered()
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H A D | genome-write.c | 207 char complCode[128] = COMPLEMENT_LC; in make_complement_buffered() local 212 complement[j] = complCode[(int) sequence[i]]; in make_complement_buffered()
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H A D | shortread.c | 1921 static char complCode[128] = COMPLEMENT_LC; variable 1930 complement[j] = complCode[(int) sequence[i]]; in make_complement() 5564 fprintf(stderr,"%c",complCode[(int) this->contents[i]]); in stderr_oneline_revcomp() 5567 fprintf(stderr,"%c",complCode[(int) this->chop[i]]); in stderr_oneline_revcomp() 5748 FPRINTF(fp,"%c",complCode[(int) this->contents[i]]); in Shortread_print_oneline_revcomp() 5756 FPRINTF(fp,"%c",complCode[(int) this->chop[i]]); in Shortread_print_oneline_revcomp() 5794 FPRINTF(fp,"%c",complCode[(int) this->contents[i]]); in Shortread_print_chopped_revcomp_sam() 5840 FPRINTF(fp,"%c",complCode[(int) this->contents[i]]); in Shortread_print_chopped_end_revcomp() 5849 FPRINTF(fp,"%c",complCode[(int) this->contents[i]]); in Shortread_print_chopped_end_revcomp() 5937 FPRINTF(fp,"%c",complCode[(int) this->chop[i]]); in Shortread_print_chop() [all …]
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H A D | translation.c | 70 static char complCode[128] = COMPLEMENT_UC; variable 896 nt0 = revcompp ? complCode[(int) pair->genome] : uppercaseCode[(int) pair->genome]; in translate_pairs_forward() 938 nt0 = revcompp ? complCode[(int) pair->genome] : uppercaseCode[(int) pair->genome]; in translate_pairs_backward() 1169 nt2 = revcompp ? complCode[(int) pairs[j].cdna] : uppercaseCode[(int) pairs[j].cdna]; in get_codon_forward() 1217 nt2 = revcompp ? complCode[(int) pairs[j].cdna] : uppercaseCode[(int) pairs[j].cdna]; in get_codon_backward()
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H A D | dynprog_end.c | 581 static char complCode[128] = COMPLEMENT_LC; variable 644 debug8(printf("At %u, genomicnt is %c\n",genomicpos,complCode[(int) c2])); in get_genomic_nt() 645 *g_alt = complCode[(int) c2_alt]; in get_genomic_nt() 646 return complCode[(int) c2]; in get_genomic_nt() 2449 temp = complCode[(int) sequence[i]]; in make_complement_inplace() 2450 sequence[i] = complCode[(int) sequence[j]]; in make_complement_inplace() 2454 sequence[i] = complCode[(int) sequence[i]]; in make_complement_inplace()
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H A D | dynprog.c | 137 static char complCode[128] = COMPLEMENT_LC; variable 199 debug8(printf("At %u, genomicnt is %c\n",genomicpos,complCode[(int) c2])); in get_genomic_nt() 200 *g_alt = complCode[(int) c2_alt]; in get_genomic_nt() 201 return complCode[(int) c2]; in get_genomic_nt()
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H A D | samprint.c | 75 static char complCode[128] = COMPLEMENT_LC; variable 897 *donor2 = toupper(complCode[(int) genomic[substring_start-2]]); in halfdonor_dinucleotide() 898 *donor1 = toupper(complCode[(int) genomic[substring_start-1]]); in halfdonor_dinucleotide() 924 *acceptor1 = toupper(complCode[(int) genomic[substring_end]]); in halfacceptor_dinucleotide() 925 *acceptor2 = toupper(complCode[(int) genomic[substring_end+1]]); in halfacceptor_dinucleotide()
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H A D | genome.c | 411 static char complCode[128] = COMPLEMENT_LC; variable 419 complement[j] = complCode[(int) sequence[i]]; 432 temp = complCode[(int) sequence[i]]; in make_complement_inplace() 433 sequence[i] = complCode[(int) sequence[j]]; in make_complement_inplace() 437 sequence[i] = complCode[(int) sequence[i]]; in make_complement_inplace()
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H A D | stage1hr.c | 967 static char complCode[128] = COMPLEMENT_LC; variable 975 complement[j] = complCode[(int) sequence[i]]; in make_complement_buffered() 989 temp = complCode[(int) sequence[i]]; 990 sequence[i] = complCode[(int) sequence[j]]; 994 sequence[i] = complCode[(int) sequence[i]];
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H A D | dynprog_genome.c | 207 static char complCode[128] = COMPLEMENT_LC; 269 debug8(printf("At %u, genomicnt is %c\n",genomicpos,complCode[(int) c2])); 270 *g_alt = complCode[(int) c2_alt]; 271 return complCode[(int) c2];
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H A D | substring.c | 195 static char complCode[128] = COMPLEMENT_LC; variable 203 temp = complCode[(int) sequence[i]]; in make_complement_inplace() 204 sequence[i] = complCode[(int) sequence[j]]; in make_complement_inplace() 208 sequence[i] = complCode[(int) sequence[i]]; in make_complement_inplace() 4712 FPRINTF(fp,"%c",(char) tolower(complCode[(int) nt[i]])); in print_revcomp_lc()
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H A D | cigar.c | 571 static char complCode[128] = COMPLEMENT_LC; variable 579 complement[j] = complCode[(int) sequence[i]]; in make_complement_buffered()
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