Home
last modified time | relevance | path

Searched refs:complCode (Results 1 – 25 of 29) sorted by relevance

12

/dports/biology/gmap/gmap-2020-09-12/src/
H A Djunction.c373 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()
H A Dfilestring.c322 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()
H A Dboyer-moore.c356 static char complCode[128] = COMPLEMENT_LC;
384 *g_alt = complCode[(int) c2_alt];
385 return complCode[(int) c2];
H A Dmdprint.c23 static char complCode[128] = COMPLEMENT_LC; variable
31 complement[j] = complCode[(int) sequence[i]]; in make_complement_buffered()
H A Dsequence.c1014 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()
H A Dsimplepair.c1137 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()
H A Dpair.c820 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 …]
H A Dchimera.c635 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()
H A Dpairpool.c1014 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()
H A Dget-genome.c544 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()
H A Ddynprog_cdna.c68 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()
H A Ddynprog_single.c105 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()
H A Dsam_sort.c216 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()
H A Diit_get.c167 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()
H A Dgenome-write.c207 char complCode[128] = COMPLEMENT_LC; in make_complement_buffered() local
212 complement[j] = complCode[(int) sequence[i]]; in make_complement_buffered()
H A Dshortread.c1921 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 …]
H A Dtranslation.c70 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()
H A Ddynprog_end.c581 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()
H A Ddynprog.c137 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()
H A Dsamprint.c75 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()
H A Dgenome.c411 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()
H A Dstage1hr.c967 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]];
H A Ddynprog_genome.c207 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];
H A Dsubstring.c195 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()
H A Dcigar.c571 static char complCode[128] = COMPLEMENT_LC; variable
579 complement[j] = complCode[(int) sequence[i]]; in make_complement_buffered()

12