| /dports/biology/gmap/gmap-2020-09-12/src/ |
| H A D | splice.c | 83 static Genome_T genomebits_alt; variable
92 genomebits_alt = genomebits_alt_in; in Splice_setup()
336 genomebits,genomebits_alt,query_compress,/*left*/segmenti_left, in Splice_resolve_sense()
340 genomebits,genomebits_alt,query_compress,/*left*/segmentj_left, in Splice_resolve_sense()
611 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in Splice_resolve_sense()
659 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in Splice_resolve_sense()
726 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in Splice_resolve_sense()
774 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in Splice_resolve_sense()
878 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in Splice_resolve_sense()
926 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in Splice_resolve_sense()
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| H A D | distant-dna.c | 36 static Genome_T genomebits_alt; variable
183 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_fwd, in Distant_dna_solve()
214 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_fwd, in Distant_dna_solve()
362 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_rev, in Distant_dna_solve()
396 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_rev, in Distant_dna_solve()
611 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_fwd, in Distant_dna_solve()
642 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_rev, in Distant_dna_solve()
741 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_rev, in Distant_dna_solve()
775 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_fwd, in Distant_dna_solve()
901 genomebits_alt = genomebits_alt_in; in Distant_dna_setup()
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| H A D | distant-rna.c | 46 static Genome_T genomebits_alt; variable
217 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in find_spliceends_rna_plus()
271 …hes == Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_compress… in find_spliceends_rna_plus()
320 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in find_spliceends_rna_plus()
450 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in find_spliceends_rna_plus()
553 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in find_spliceends_rna_plus()
733 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in find_spliceends_rna_minus()
837 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in find_spliceends_rna_minus()
968 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in find_spliceends_rna_minus()
1072 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in find_spliceends_rna_minus()
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| H A D | indel.c | 31 static Genome_T genomebits_alt; variable
46 genomebits_alt = genomebits_alt_in; in Indel_setup()
343 …Genome_count_mismatches_substring(&(*best_ref_nmismatches_i),genomebits,genomebits_alt,query_compr… in Indel_resolve_middle_insertion()
346 …Genome_count_mismatches_substring(&(*best_ref_nmismatches_j),genomebits,genomebits_alt,query_compr… in Indel_resolve_middle_insertion()
638 …Genome_count_mismatches_substring(&(*best_ref_nmismatches_i),genomebits,genomebits_alt,query_compr… in Indel_resolve_middle_deletion()
641 …Genome_count_mismatches_substring(&(*best_ref_nmismatches_j),genomebits,genomebits_alt,query_compr… in Indel_resolve_middle_deletion()
1051 …Genome_count_mismatches_substring(&(*best_ref_nmismatches_i),genomebits,genomebits_alt,query_compr… in Indel_resolve_middle_deletion_or_splice()
1054 …Genome_count_mismatches_substring(&(*best_ref_nmismatches_j),genomebits,genomebits_alt,query_compr… in Indel_resolve_middle_deletion_or_splice()
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| H A D | gsnap.c | 228 static Genome_T genomebits_alt = NULL; variable
3437 Path_solve_setup(genomelength,circularp,genomebits,genomebits_alt,regiondb,regiondb2, in worker_setup()
3443 genomebits,genomebits_alt,indexdb,indexdb2,indexdb_tr, in worker_setup()
3446 genomebits,genomebits_alt,indexdb,indexdb2, in worker_setup()
3457 Distant_dna_setup(genomebits,genomebits_alt,genomelength,shortsplicedist,splicingp); in worker_setup()
3464 …nome_hr_setup(Genome_blocks(genomebits),/*snp_blocks*/genomebits_alt ? Genome_blocks(genomebits_al… in worker_setup()
3485 Splice_setup(genomebits,genomebits_alt,min_shortend); in worker_setup()
3486 Indel_setup(genomebits,genomebits_alt,genomelength,transcriptomelength, in worker_setup()
3495 chromosome_iit,nchromosomes,genomecomp,genomebits,genomebits_alt, in worker_setup()
3505 invert_first_p,invert_second_p,genomecomp,genomebits,genomebits_alt, in worker_setup()
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| H A D | substring.c | 179 static Genome_T genomebits_alt; variable
1173 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in Substring_trim_qstart_nosplice()
1253 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in Substring_trim_qend_nosplice()
2074 … Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_compress,left, in Substring_new()
2101 … Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_compress,left, in Substring_new()
2944 best_loglik = MAPQ_loglik(/*ome*/genomebits,/*ome_alt*/genomebits_alt, in Substring_compute_mapq()
2950 if ((loglik = MAPQ_loglik(/*ome*/genomebits,/*ome_alt*/genomebits_alt, in Substring_compute_mapq()
2959 best_loglik = MAPQ_loglik(/*ome*/genomebits,/*ome_alt*/genomebits_alt, in Substring_compute_mapq()
2965 if ((loglik = MAPQ_loglik(/*ome*/genomebits,/*ome_alt*/genomebits_alt, in Substring_compute_mapq()
2978 this->mapq_loglik = MAPQ_loglik(/*ome*/genomebits,/*ome_alt*/genomebits_alt, in Substring_compute_mapq()
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| H A D | terminal.c | 34 static Genome_T genomebits_alt; variable
517 genomebits_alt = genomebits_alt_in; in Terminal_setup()
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| H A D | kmer-search.c | 181 static Genome_T genomebits_alt; variable
1230 …Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_compress_fwd,le… in single_hits_gplus()
1374 …Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_compress_rev,le… in single_hits_gminus()
5314 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_fwd, in combine_ends_plus()
5429 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_fwd, in combine_ends_plus()
5504 …Genome_count_mismatches_substring(&ref_nmismatches2,genomebits,genomebits_alt,query_compress_fwd,l… in combine_ends_plus()
5535 …Genome_count_mismatches_substring(&ref_nmismatches1,genomebits,genomebits_alt,query_compress_fwd,l… in combine_ends_plus()
5588 …Genome_count_mismatches_substring(&ref_nmismatches2,genomebits,genomebits_alt,query_compress_fwd,l… in combine_ends_plus()
5843 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_rev, in combine_ends_minus()
5958 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress_rev, in combine_ends_minus()
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| H A D | extension-search.c | 99 static Genome_T genomebits_alt; variable
107 static Genome_T genomebits_alt; variable
147 genomebits_alt = genomebits_alt_in; in Extension_search_setup()
152 genomebits_alt = genomebits_alt_in; in Extension_search_setup()
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| H A D | path-solve.c | 84 static Genome_T genomebits_alt; variable
557 …nmismatches = Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_c… in attach_qstart_diagonal()
583 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in attach_qstart_diagonal()
625 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in attach_qstart_diagonal()
1550 …nmismatches = Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_c… in attach_qend_diagonal()
1577 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in attach_qend_diagonal()
1619 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in attach_qend_diagonal()
4021 genomebits_alt = genomebits_alt_in; in Path_solve_setup()
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| H A D | stage3hr.c | 191 static Genome_T genomebits_alt; variable
269 genomebits_alt = genomebits_alt_in; in Stage3hr_setup()
4070 … Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_compress,left, in Stage3end_nmatches_substrings()
4073 …assert(nmismatches == Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt… in Stage3end_nmatches_substrings()
4077 …nmismatches = Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_c… in Stage3end_nmatches_substrings()
4177 …nmismatches = Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_c… in Stage3end_nmatches_substrings()
4412 … Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_compress,left, in Stage3end_new_substrings()
4419 …nmismatches = Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_c… in Stage3end_new_substrings()
4523 …nmismatches = Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_c… in Stage3end_new_substrings()
5028 …nmismatches = Genome_count_mismatches_substring(&ref_nmismatches,genomebits,genomebits_alt,query_c… in Stage3end_new_substitution()
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| H A D | stage1hr.c | 172 static Genome_T genomebits_alt; variable
3068 genomebits_alt = genomebits_alt_in; in Stage1hr_setup()
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