/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | intron.c | 26 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,
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H A D | dynprog_simd.h | 22 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,
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H A D | dynprog_single.c | 129 } 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 …]
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H A D | dynprog_end.h | 29 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,
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H A D | stage3.c | 457 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 …]
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H A D | dynprog_genome.c | 231 } 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 …]
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H A D | dynprog_end.c | 606 } 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 …]
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H A D | stage2.h | 53 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,
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H A D | substring.h | 67 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 …]
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H A D | dynprog_cdna.c | 92 } 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 …]
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H A D | stage2.c | 719 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 …]
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H A D | substring.c | 247 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 …]
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H A D | splicetrie.c | 174 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 …]
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H A D | segment-search.c | 507 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 …]
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H A D | dynprog.c | 161 } 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 …]
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H A D | terminal.c | 84 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()
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H A D | dynprog.h | 240 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,
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H A D | distant-rna.c | 169 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 …]
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H A D | path-solve.c | 1069 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 …]
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H A D | diag.h | 52 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp); 56 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp);
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H A D | boyer-moore.c | 360 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()
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H A D | dynprog_single.h | 26 Univcoord_T chroffset, Univcoord_T chrhigh, 39 Univcoord_T chroffset, Univcoord_T chrhigh,
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H A D | splicetrie_build.c | 452 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 …]
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/dports/emulators/mednafen/mednafen/src/nes/boards/ |
H A D | 90.cpp | 38 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()
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/dports/games/libretro-fceumm/libretro-fceumm-91ccd3b/src/boards/ |
H A D | 90.c | 49 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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