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Searched refs:query_compress (Results 1 – 23 of 23) sorted by relevance

/dports/biology/gmap/gmap-2020-09-12/src/
H A Dgenome128_hr.h16 Genome_count_mismatches_substring_ref (Genome_T ome, Compress_T query_compress, Univcoord_T left,
19 …smatches_substring (int *ref_mismatches, Genome_T ome, Genome_T ome_alt, Compress_T query_compress,
24 Genome_T ome, Genome_T ome_alt, Compress_T query_compress,
28 Genome_T ome, Genome_T ome_alt, Compress_T query_compress,
32 Genome_T ome, Genome_T ome_alt, Compress_T query_compress,
36 Genome_T ome, Genome_T ome_alt, Compress_T query_compress,
40 Genome_first_kmer_left (int *nmismatches5, Genome_T ome, Compress_T query_compress,
44 Genome_first_kmer_right (int *nmismatches3, Genome_T ome, Compress_T query_compress,
49 Genome_mark_mismatches_ref (char *genomic, int querylength, Compress_T query_compress,
53 Genome_mark_mismatches (char *genomic, int querylength, Compress_T query_compress,
H A Dsubstring.h63 Compress_T query_compress, Univcoord_T left, Univcoord_T chroffset,
67 Compress_T query_compress, Univcoord_T left, Univcoord_T chrhigh,
73 bool plusp, int genestrand, int *mismatch_positions_alloc, Compress_T query_compress,
78 int *mismatch_positions_alloc, Compress_T query_compress,
84 bool plusp, int genestrand, int *mismatch_positions_alloc, Compress_T query_compress,
90 int *mismatch_positions_alloc, Compress_T query_compress,
96 bool plusp, int genestrand, Compress_T query_compress,
110 Compress_T query_compress);
113 Compress_T query_compress);
117 bool plusp, int genestrand, Compress_T query_compress,
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H A Dindel.h23 Genome_T ome, Genome_T ome_alt, Compress_T query_compress,
34 Genome_T ome, Genome_T ome_alt, Compress_T query_compress,
43 Genome_T ome, Genome_T ome_alt, Compress_T query_compress,
51 int querylength, Compress_T query_compress,
59 int querylength, Compress_T query_compress,
H A Dindel.c107 ome,ome_alt,query_compress,left,pos5,pos3, in Indel_resolve_middle_insertion()
135 ome,ome_alt,query_compress,left-indels,pos5,pos3, in Indel_resolve_middle_insertion()
425 ome,ome_alt,query_compress,left,pos5,pos3, in Indel_resolve_middle_deletion()
452 ome,ome_alt,query_compress,left-indels,pos5,pos3, in Indel_resolve_middle_deletion()
748 ome,ome_alt,query_compress,left,pos5,pos3, in Indel_resolve_middle_deletion_or_splice()
1087 int querylength, Compress_T query_compress, in Indel_solve_end_low() argument
1166 omebits,omebits_alt,query_compress, in Indel_solve_end_low()
1190 omebits,omebits_alt,query_compress, in Indel_solve_end_low()
1221 int querylength, Compress_T query_compress, in Indel_solve_end_high() argument
1300 omebits,omebits_alt,query_compress, in Indel_solve_end_high()
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H A Ddistant-rna.c143 Compress_T query_compress, Listpool_T listpool, in find_spliceends_rna_plus() argument
217 /*ome*/genomebits,/*ome_alt*/genomebits_alt,query_compress, in find_spliceends_rna_plus()
238 /*left*/segment_left,query_compress, in find_spliceends_rna_plus()
341 /*left*/segment_left,query_compress, in find_spliceends_rna_plus()
471 /*left*/segment_left,query_compress, in find_spliceends_rna_plus()
574 /*left*/segment_left,query_compress, in find_spliceends_rna_plus()
659 Compress_T query_compress, Listpool_T listpool, in find_spliceends_rna_minus() argument
754 /*left*/segment_left,query_compress, in find_spliceends_rna_minus()
858 /*left*/segment_left,query_compress, in find_spliceends_rna_minus()
989 /*left*/segment_left,query_compress, in find_spliceends_rna_minus()
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H A Dterminal.c64 Compress_T query_compress, Listpool_T listpool, in find_terminals() argument
142 query_compress,segment_left,chroffset, 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()
211 query_compress,segment_left,chroffset, 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 Dpath-solve.c1068 querylength,plusp,genestrand,query_compress, in combine_into_qstart_alts()
1075 querylength,plusp,genestrand,query_compress, in combine_into_qstart_alts()
1083 querylength,plusp,genestrand,query_compress, in combine_into_qstart_alts()
1090 querylength,plusp,genestrand,query_compress, in combine_into_qstart_alts()
1517 mismatch_positions_alloc,query_compress, in attach_qend_diagonal()
2394 querylength,plusp,genestrand,query_compress, in add_qend_local()
3608 mismatch_positions_alloc,query_compress, in Path_solve_from_diagonals()
3695 mismatch_positions_alloc,query_compress, in Path_solve_from_diagonals()
3805 mismatch_positions_alloc,query_compress, in Path_solve_from_diagonals()
3849 stream_alloc,streamsize_alloc,query_compress, in Path_solve_from_diagonals()
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H A Dsubstring.c1856 new->query_compress = query_compress; in Substring_new()
2151 Compress_T query_compress) { in Substring_extend_anchor_querystart() argument
2167 mismatch_positions_alloc,query_compress, in Substring_extend_anchor_querystart()
2260 Compress_T query_compress) { in Substring_extend_anchor_queryend() argument
2276 mismatch_positions_alloc,query_compress, in Substring_extend_anchor_queryend()
2404 new->query_compress = query_compress;
2621 new->query_compress = query_compress; in Substring_new_alts_D()
2740 new->query_compress = query_compress; in Substring_new_alts_A()
2945 this->query_compress,left,mapq_start,mapq_end, in Substring_compute_mapq()
2960 this->query_compress,left,mapq_start,mapq_end, in Substring_compute_mapq()
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H A Dsplice.c201 int pos5, int pos3, int querylength, Compress_T query_compress, in Splice_resolve_sense() argument
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()
1112 int pos5, int pos3, int querylength, Compress_T query_compress, in Splice_resolve_antisense() argument
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H A Dgenome128_consec.h15 Genome_consecutive_matches_rightward (Genome_T ome, Compress_T query_compress, Univcoord_T left, in…
18 Genome_consecutive_matches_leftward (Genome_T ome, Compress_T query_compress, Univcoord_T left, int…
H A Dsplice.h64 int pos5, int pos3, int querylength, Compress_T query_compress,
78 int pos5, int pos3, int querylength, Compress_T query_compress,
H A Dmapq.c155 MAPQ_loglik (Genome_T ome, Genome_T ome_alt, Compress_T query_compress, in MAPQ_loglik() argument
194 ome,ome_alt,query_compress,left,/*pos5*/querystart,/*pos3*/queryend, in MAPQ_loglik()
230 ome,ome_alt,query_compress,left,/*pos5*/querylength - queryend, in MAPQ_loglik()
H A Dextension-search.c354 Compress_T query_compress, bool plusp, int genestrand) { in Elt_read_queryfwd() argument
384 Genome_consecutive_matches_rightward(genomebits,query_compress,left, in Elt_read_queryfwd()
439 Compress_T query_compress, bool plusp, int genestrand) { in Elt_read_queryrev() argument
469 Genome_consecutive_matches_leftward(genomebits,query_compress,left, in Elt_read_queryrev()
519 Elt_set_queryfwd_extend_left (List_T list, Compress_T query_compress,
545 Genome_consecutive_matches_leftward(genomebits,query_compress,left,
589 Compress_T query_compress, bool plusp, int genestrand) {
1589 int *mismatch_positions_alloc, Compress_T query_compress, in extend_seeds() argument
1651 query_compress,nmismatches_allowed, in extend_seeds()
1668 query_compress,nmismatches_allowed, in extend_seeds()
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H A Ddynprog_end.h95 int cutoff_level, char *queryptr, int querylength, Compress_T query_compress,
111 int cutoff_level, char *queryptr, int querylength, Compress_T query_compress,
H A Dgenome128_hr.c4286 query_shifted = Compress_shift(query_compress,nshift);
4480 query_shifted = Compress_shift(query_compress,nshift);
4689 query_shifted = Compress_shift(query_compress,nshift); in Genome_count_mismatches_substring_ref()
4865 query_shifted = Compress_shift(query_compress,nshift); in count_mismatches_substring_snps()
5201 query_shifted = Compress_shift(query_compress,nshift); in mismatches_left()
5423 Compress_T query_compress, in mismatches_left_alt() argument
5691 Compress_T query_compress, in Genome_mismatches_left() argument
5723 Compress_T query_compress, in Genome_mismatches_left_trim() argument
6013 Compress_T query_compress, in mismatches_right_alt() argument
6278 Compress_T query_compress, in Genome_mismatches_right() argument
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H A Dmapq.h19 MAPQ_loglik (Genome_T ome, Genome_T ome_alt, Compress_T query_compress,
H A Dregiondb.c907 Compress_T query_compress, int pos5, int pos3, Genome_T genomebits,
959 …trim_ends(&trim5,&trim3,&nmismatches5,&nmismatches3,poly_p,query_compress,left,querylength,genomeb…
961 querystart = Genome_first_kmer_left(&nmismatches5,genomebits,query_compress,left,pos5,pos3,
963 queryend = Genome_first_kmer_right(&nmismatches3,genomebits,query_compress,left,pos5,pos3,
997 …trim_ends(&trim5,&trim3,&nmismatches5,&nmismatches3,poly_p,query_compress,left,querylength,genomeb…
999 querystart = Genome_first_kmer_left(&nmismatches5,genomebits,query_compress,left,pos5,pos3,
1001 queryend = Genome_first_kmer_right(&nmismatches3,genomebits,query_compress,left,pos5,pos3,
1033 …trim_ends(&trim5,&trim3,&nmismatches5,&nmismatches3,poly_p,query_compress,left,querylength,genomeb…
1035 querystart = Genome_first_kmer_left(&nmismatches5,genomebits,query_compress,left,pos5,pos3,
1037 queryend = Genome_first_kmer_right(&nmismatches3,genomebits,query_compress,left,pos5,pos3,
H A Dpath-solve.h37 Univcoord_T **stream_alloc, int *streamsize_alloc, Compress_T query_compress,
H A Dstage3hr.h315 int querylength, Compress_T query_compress,
323 int querylength, Compress_T query_compress,
334 int *mismatch_positions_alloc, Compress_T query_compress,
H A Dstage3hr.c3967 int querylength, Compress_T query_compress, in Stage3end_nmatches_substrings() argument
4200 /*plusp*/false,genestrand,query_compress, in Stage3end_nmatches_substrings()
4307 int querylength, Compress_T query_compress, in Stage3end_new_substrings() argument
4429 /*plusp*/true,genestrand,query_compress, in Stage3end_new_substrings()
4534 /*plusp*/false,genestrand,query_compress, in Stage3end_new_substrings()
4989 int *mismatch_positions_alloc, Compress_T query_compress, in Stage3end_new_substitution() argument
5010 mismatch_positions_alloc,query_compress,chroffset,sensedir); in Stage3end_new_substitution()
5013 mismatch_positions_alloc,query_compress,chroffset,chrhigh,sensedir); in Stage3end_new_substitution()
5035 querylength,/*plusp*/true,genestrand,query_compress, in Stage3end_new_substitution()
5052 mismatch_positions_alloc,query_compress,chroffset,sensedir); in Stage3end_new_substitution()
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H A Dsegment-search.c1102 Univcoord_T **stream_alloc, int *streamsize_alloc, Compress_T query_compress, in solve_all() argument
1320 … query_compress,chrnum,anchor_segment->chroffset,anchor_segment->chrhigh,anchor_segment->chrlength, in solve_all()
H A Dgenome128_consec.c3242 Genome_consecutive_matches_rightward (Genome_T ome, Compress_T query_compress, Univcoord_T left, in… in Genome_consecutive_matches_rightward() argument
3279 query_shifted = Compress_shift(query_compress,nshift); in Genome_consecutive_matches_rightward()
3508 Genome_consecutive_matches_leftward (Genome_T ome, Compress_T query_compress, Univcoord_T left, int… in Genome_consecutive_matches_leftward() argument
3550 query_shifted = Compress_shift(query_compress,nshift); in Genome_consecutive_matches_leftward()
/dports/biology/gmap/gmap-2020-09-12/
H A DChangeLog13661 * stage1hr.c: Computing query_compress if necessary before deciding whether
15900 substring.h: Marking all mismatches by using query_compress,
16373 * stage1hr.c: Added check for query_compress to be non-NULL before
16376 * stage1hr.c: Fixed bug where query_compress needed to be computed before