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Searched refs:chrhigh (Results 1 – 25 of 55) sorted by relevance

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/dports/biology/gmap/gmap-2020-09-12/src/
H A Dintron.c26 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
60 cdna_direction,watsonp,chrhigh-leftgenomepos,chrhigh-leftgenomepos+1U));
62 chrhigh-leftgenomepos,chrhigh-leftgenomepos+1U,
82 cdna_direction,watsonp,chrhigh-leftgenomepos,chrhigh-leftgenomepos+1U));
84 chrhigh-leftgenomepos,chrhigh-leftgenomepos+1U,
123 chrhigh-rightgenomepos,chrhigh-rightgenomepos+1U,
141 chrhigh-rightgenomepos,chrhigh-rightgenomepos+1U,
H A Ddynprog_simd.h22 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
32 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
42 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
53 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
63 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
73 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
83 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int genestrand,
91 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int genestrand,
106 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int genestrand,
114 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int genestrand,
H A Ddynprog_single.c129 } else if (pos >= chrhigh) { in get_genomic_nt()
153 } else if (pos >= chrhigh) { in get_genomic_nt()
434 Univcoord_T chroffset, Univcoord_T chrhigh, in Dynprog_single_gap() argument
559 glength,chrhigh,/*revcomp*/false); in Dynprog_single_gap()
592 goffset,chroffset,chrhigh,watsonp, in Dynprog_single_gap()
609 goffset,chroffset,chrhigh,watsonp, in Dynprog_single_gap()
1083 chroffset,chrhigh,watsonp); in Dynprog_microexon_int()
1118 splicesitepos = chrhigh - (candidate-1); in Dynprog_microexon_int()
1123 splicesitepos = chrhigh - (candidate-1); in Dynprog_microexon_int()
1292 chroffset,chrhigh,watsonp);
[all …]
H A Ddynprog_end.h29 Univcoord_T chroffset, Univcoord_T chrhigh,
40 Univcoord_T chroffset, Univcoord_T chrhigh,
49 Univcoord_T chroffset, Univcoord_T chrhigh,
60 Univcoord_T chroffset, Univcoord_T chrhigh,
77 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, Pairpool_T pairpool);
81 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, Pairpool_T pairpool);
91 Univcoord_T chroffset, Univcoord_T chrhigh,
107 Univcoord_T chroffset, Univcoord_T chrhigh,
H A Dstage3.c457 Univcoord_T chrhigh; member
478 return this->chrhigh; in Stage3middle_chrhigh()
519 new->chrhigh = chrhigh; in Stage3middle_new()
764 return this->chrhigh; in Stage3_chrhigh()
6005 new->chrhigh = chrhigh; in Stage3_new()
6162 new->chrhigh = old->chrhigh;
6767 int chrlow, chrhigh; in print_map() local
12193 chroffset,chrhigh, in build_pairs_introns()
13927 chroffset,chrhigh, in path_compute_end5()
13973 chroffset,chrhigh, in path_compute_end5()
[all …]
H A Ddynprog_genome.c231 } else if (pos >= chrhigh) {
255 } else if (pos >= chrhigh) {
386 splicesitepos = chrhigh - rightoffset + cR; in get_splicesite_probs()
573 (chrhigh - chroffset) - rightoffset, in get_known_splicesites()
1030 splicesitepos = chrhigh - rightoffset + cR; in bridge_intron_gap_8_site_level()
1051 splicesitepos = chrhigh - rightoffset + cR; in bridge_intron_gap_8_site_level()
1904 splicesitepos = chrhigh - rightoffset + cR; in bridge_intron_gap_16_site_level()
1925 splicesitepos = chrhigh - rightoffset + cR; in bridge_intron_gap_16_site_level()
3511 goffsetL,chroffset,chrhigh,watsonp, in Dynprog_genome_gap()
3519 goffsetL,chroffset,chrhigh,watsonp, in Dynprog_genome_gap()
[all …]
H A Ddynprog_end.c606 } else if (pos >= chrhigh) { in get_genomic_nt()
630 } else if (pos >= chrhigh) { in get_genomic_nt()
1371 glength,chrhigh,/*revcomp*/true); in Dynprog_end5_gap()
1536 chroffset,chrhigh,watsonp, in Dynprog_end5_gap()
1969 glength,chrhigh,/*revcomp*/false); in Dynprog_end3_gap()
1991 goffset,chroffset,chrhigh,watsonp, in Dynprog_end3_gap()
1998 goffset,chroffset,chrhigh,watsonp, in Dynprog_end3_gap()
2045 goffset,chroffset,chrhigh,watsonp, in Dynprog_end3_gap()
2119 chroffset,chrhigh,watsonp, in Dynprog_end3_gap()
2796 low = chrhigh - rev_goffset; in Dynprog_end5_known()
[all …]
H A Dstage2.h53 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
60 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
73 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
82 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
91 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
H A Dsubstring.h67 Compress_T query_compress, Univcoord_T left, Univcoord_T chrhigh,
85 Univcoord_T chroffset, Univcoord_T chrhigh, int sensedir);
91 Univcoord_T chroffset, Univcoord_T chrhigh, int sensedir);
97 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
103 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
118 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
126 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
314 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength);
322 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength);
332 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength);
[all …]
H A Ddynprog_cdna.c92 } else if (pos >= chrhigh) { in get_genomic_nt()
116 } else if (pos >= chrhigh) { in get_genomic_nt()
942 glength,chrhigh,/*revcomp*/false); in Dynprog_cdna_gap()
945 glength,chrhigh,/*revcomp*/true); in Dynprog_cdna_gap()
964 goffset,chroffset,chrhigh,watsonp, in Dynprog_cdna_gap()
971 goffset,chroffset,chrhigh,watsonp, in Dynprog_cdna_gap()
981 rev_goffset,chroffset,chrhigh,watsonp, in Dynprog_cdna_gap()
989 rev_goffset,chroffset,chrhigh,watsonp, in Dynprog_cdna_gap()
1093 goffset,chroffset,chrhigh,watsonp, in Dynprog_cdna_gap()
1100 goffset,chroffset,chrhigh,watsonp, in Dynprog_cdna_gap()
[all …]
H A Dstage2.c719 leftpos,rightpos,chroffset,chrhigh));
762 if (leftpos > chrhigh - 3) {
763 leftpos = chrhigh - 3;
766 if (rightpos > chrhigh - 3) {
767 rightpos = chrhigh - 3;
814 chrhigh-chroffset-(leftpos-leftmiss),chrhigh-chroffset-(rightpos-rightmiss)));
4366 chroffset,chrhigh,plusp, in align_compute_lookback()
4770 chroffset,chrhigh,plusp, in align_compute_scores_lookforward()
5046 chroffset,chrhigh,plusp, in align_compute_lookforward()
6863 chroffset,chrhigh,plusp, in Stage2_compute()
[all …]
H A Dsubstring.c247 Univcoord_T chrhigh; member
1659 if (alignend <= chrhigh) { in Substring_compute_nmatches()
1718 if (alignend <= chrhigh) { in Substring_compute_nmatches()
1763 if (alignstart <= chrhigh) { in Substring_compute_nmatches()
1962 if (alignend <= chrhigh) { in Substring_new()
2022 new->chrhigh = chrhigh; in Substring_new()
2452 new->chrhigh = chrhigh;
2594 new->chrhigh = chrhigh; in Substring_new_alts_D()
2713 new->chrhigh = chrhigh; in Substring_new_alts_A()
3507 return this->chrhigh; in Substring_chrhigh()
[all …]
H A Dsplicetrie.c174 Univcoord_T chroffset, Univcoord_T chrhigh, in solve_end5_aux() argument
395 chroffset,chrhigh,&(*dynprogindex),dynprog, in solve_end5_aux()
407 chroffset,chrhigh,&(*dynprogindex),dynprog, in solve_end5_aux()
419 chroffset,chrhigh,&(*dynprogindex),dynprog, in solve_end5_aux()
431 chroffset,chrhigh,&(*dynprogindex),dynprog, in solve_end5_aux()
454 Univcoord_T chroffset, Univcoord_T chrhigh, in solve_end3_aux() argument
669 chroffset,chrhigh,&(*dynprogindex),dynprog, in solve_end3_aux()
681 chroffset,chrhigh,&(*dynprogindex),dynprog, in solve_end3_aux()
693 chroffset,chrhigh,&(*dynprogindex),dynprog, in solve_end3_aux()
757 chroffset,chrhigh,&(*dynprogindex),dynprog, in Splicetrie_solve_end5()
[all …]
H A Dsegment-search.c507 Univcoord_T chrhigh = 0; in make_records() local
595 chrhigh = Univ_IIT_update_chrnum(&chrnum,&chroffset,chrhigh,&chrlength,chromosome_iit, in make_records()
602 if (diagonal >= chrhigh) { in make_records()
618 chrhigh = chrhighs[chrnum-1]; in make_records()
642 most_inbounds = chrhigh - diagonal; in make_records()
663 chrhigh = chrhighs[chrnum-1]; in make_records()
678 diagonal,querylength,chrnum,chrhigh)); in make_records()
698 if (left + record->queryend > chrhigh) { in make_records()
700 left,record->queryend,chrhigh)); in make_records()
711 record->chrhigh = chrhigh; in make_records()
[all …]
H A Ddynprog.c161 } else if (pos >= chrhigh) { in get_genomic_nt()
185 } else if (pos >= chrhigh) { in get_genomic_nt()
241 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, in Dynprog_Matrix32_print() argument
350 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, in Matrix3_print() argument
517 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, in Dynprog_Directions32_print() argument
1702 goffset,chroffset,chrhigh,watsonp,revp,lband,uband)); in Dynprog_standard()
1705 goffset,chroffset,chrhigh,watsonp,revp,lband,uband)); in Dynprog_standard()
1707 goffset,chroffset,chrhigh,watsonp,revp)); in Dynprog_standard()
1756 queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh, in Dynprog_traceback_std()
1812 genomeoffset,genomecoord,chroffset,chrhigh,watsonp)); in Dynprog_traceback_std()
[all …]
H A Dterminal.c84 Univcoord_T chroffset, chrhigh; in find_terminals() local
127 chrnum = Univ_IIT_get_chrnum(&chroffset,&chrhigh,&chrlength,chromosome_iit, in find_terminals()
145 query_compress,segment_left,chrhigh, in find_terminals()
157 plusp,genestrand,query_compress,chrnum,chroffset,chrhigh,chrlength, in find_terminals()
171 plusp,genestrand,query_compress,chrnum,chroffset,chrhigh,chrlength, in find_terminals()
196 chrnum = Univ_IIT_get_chrnum(&chroffset,&chrhigh,&chrlength,chromosome_iit, in find_terminals()
214 query_compress,segment_left,chrhigh, in find_terminals()
226 plusp,genestrand,query_compress,chrnum,chroffset,chrhigh,chrlength, in find_terminals()
240 plusp,genestrand,query_compress,chrnum,chroffset,chrhigh,chrlength, in find_terminals()
H A Ddynprog.h240 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh,
246 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh,
253 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
263 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int genestrand,
H A Ddistant-rna.c169 Univcoord_T chroffset, chrhigh; in find_spliceends_rna_plus() local
273 if (segment_univdiagonal <= chrhigh) { in find_spliceends_rna_plus()
376 if (segment_univdiagonal <= chrhigh) { in find_spliceends_rna_plus()
506 if (segment_univdiagonal <= chrhigh) { in find_spliceends_rna_plus()
542 chroffset,chrhigh,/*sensedir*/SENSE_ANTI); in find_spliceends_rna_plus()
609 if (segment_univdiagonal <= chrhigh) { in find_spliceends_rna_plus()
685 Univcoord_T chroffset, chrhigh; in find_spliceends_rna_minus() local
789 if (segment_univdiagonal <= chrhigh) { in find_spliceends_rna_minus()
893 if (segment_univdiagonal <= chrhigh) { in find_spliceends_rna_minus()
1024 if (segment_univdiagonal <= chrhigh) { in find_spliceends_rna_minus()
[all …]
H A Dpath-solve.c1069 chrnum,chroffset,chrhigh,chrlength, in combine_into_qstart_alts()
1076 chrnum,chroffset,chrhigh,chrlength, in combine_into_qstart_alts()
1084 chrnum,chroffset,chrhigh,chrlength, in combine_into_qstart_alts()
1091 chrnum,chroffset,chrhigh,chrlength, in combine_into_qstart_alts()
1518 chroffset,chrhigh,sensedir); in attach_qend_diagonal()
2062 chrnum,chroffset,chrhigh,chrlength, in combine_into_qend_alts()
2068 chrnum,chroffset,chrhigh,chrlength, in combine_into_qend_alts()
2077 chrnum,chroffset,chrhigh,chrlength, in combine_into_qend_alts()
2083 chrnum,chroffset,chrhigh,chrlength, in combine_into_qend_alts()
2142 chrnum,chroffset,chrhigh,querylength, in compute_qend_paths()
[all …]
H A Ddiag.h52 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp);
56 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp);
H A Dboyer-moore.c360 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp) {
377 c2 = Genome_get_char(genome,chrhigh - genomicpos);
380 c2 = Genome_get_char_blocks(&c2_alt,chrhigh - genomicpos);
393 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp) { in BoyerMoore_nt() argument
408 …ht(text,text_alt,/*left*/chroffset+textoffset,/*length*/textlen+querylen,chrhigh,/*revcomp*/false); in BoyerMoore_nt()
410 …Genome_get_segment_blocks_left(text,text_alt,/*right*/chrhigh-textoffset+1,/*length*/textlen+query… in BoyerMoore_nt()
H A Ddynprog_single.h26 Univcoord_T chroffset, Univcoord_T chrhigh,
39 Univcoord_T chroffset, Univcoord_T chrhigh,
H A Dsplicetrie_build.c452 if (position >= chrhigh) { in Splicetrie_retrieve_via_splicesites()
573 if (position >= chrhigh) { in Splicetrie_retrieve_via_splicesites()
851 if (position >= chrhigh) { in Splicetrie_retrieve_via_introns()
1877 chrhigh = 0U; in Splicetrie_npartners()
1891 rightbound_min = chrhigh; in Splicetrie_npartners()
1900 rightbound_obs = chrhigh; in Splicetrie_npartners()
1911 rightbound_max = chrhigh; in Splicetrie_npartners()
2011 rightbound_min = chrhigh; in Splicetrie_npartners()
2031 rightbound_max = chrhigh; in Splicetrie_npartners()
2879 chrhigh = 0U; in build_via_introns_size()
[all …]
/dports/emulators/mednafen/mednafen/src/nes/boards/
H A D90.cpp38 static uint8 chrhigh[8]; variable
132 setchr8(chrlow[0]|(chrhigh[0]<<8)); in tekvrom()
136 setchr4(x<<10,chrlow[x]|(chrhigh[x]<<8)); in tekvrom()
140 setchr2(x<<10,chrlow[x]|(chrhigh[x]<<8)); in tekvrom()
144 setchr1(x<<10,(chrlow[x]|(chrhigh[x]<<8))); in tekvrom()
174 chrhigh[A&7]=V; in DECLFW()
282 memset(chrhigh,0xff,sizeof(chrhigh)); in M90Power()
305 SFPTR8N(chrhigh, 8, "CHRH"), in StateAction()
/dports/games/libretro-fceumm/libretro-fceumm-91ccd3b/src/boards/
H A D90.c49 static uint8 chrhigh[8]; variable
69 { chrhigh, 8, "CHRH" },
169 setchr8(((chrlow[0] | (chrhigh[0] << 8)) & mask) | bank); in tekvrom()
174 setchr4(x<<10,((chrlow[x]|(chrhigh[x]<<8))&mask)|bank); in tekvrom()
176 setchr4(0x0000, ((chrlow[chr[0]] | (chrhigh[chr[0]] << 8)) & mask) | bank); in tekvrom()
177 setchr4(0x1000, ((chrlow[chr[1]] | (chrhigh[chr[1]] << 8)) & mask) | bank); in tekvrom()
181 setchr2(x << 10, ((chrlow[x] | (chrhigh[x] << 8)) & mask) | bank); in tekvrom()
185 setchr1(x << 10, ((chrlow[x] | (chrhigh[x] << 8)) & mask) | bank); in tekvrom()
222 chrhigh[A & 7] = V; in DECLFW()
444 memset(chrhigh, 0xff, sizeof(chrhigh)); in M90Power()

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