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/dports/biology/gmap/gmap-2020-09-12/src/
H A Dindexdb-write.h23 Width_T index1part,
33 Width_T index1part,
43 Width_T index1part,
54 Width_T index1part
64 Width_T index1part
76 int index1part,
88 int index1part,
H A Dindexdb-write.c291 Width_T index1part, in Indexdb_count_offsets()
472 Width_T index1part, in Indexdb_write_offsets()
808 Width_T index1part, in Indexdb_write_offsets_huge()
1202 Width_T index1part in Indexdb_bitpack_counter()
1259 Width_T index1part in Indexdb_bitpack_counter_huge()
1388 Width_T index1part,
1634 Width_T index1part,
1911 Width_T index1part, in compute_positions()
2183 Width_T index1part, in compute_positions_huge_offsets()
2455 int index1part, in Indexdb_write_positions()
[all …]
H A Dindexdb.c131 static Width_T index1part; variable
137 index1part = index1part_in; in Indexdb_setup()
468 *index1part = 0; in Indexdb_get_filenames_no_compression()
795 *index1part = 0; in Indexdb_get_filenames_bitpack()
1698 *index1part = new->index1part; in Indexdb_new_genome()
1747 *index1part = new->index1part; in Indexdb_new_transcriptome()
2036 index1part in Indexdb_offsets_from_bitpack()
2044 index1part in Indexdb_offsets_from_bitpack()
2147 index1part in Indexdb_offsets_from_bitpack_huge()
2155 index1part in Indexdb_offsets_from_bitpack_huge()
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H A Dindexdb.h49 Indexdb_mean_size (T this, Mode_T mode, Width_T index1part);
80 Width_T *index1part, Width_T *index1interval, char *genomesubdir,
96 Width_T index1part
106 Width_T index1part
121 Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
131 Indexdb_new_transcriptome (Width_T *index1part, Width_T *index1interval,
146 Width_T index1part,
H A Dgenome-write.c126 int index1part) { in fill_zero() argument
147 int index1part) { in fill_x() argument
223 int index1part, int nmessages) { in genome_write_file() argument
301 fill_x(refgenome_fp,maxposition,startposition,uncompressedp,index1part); in genome_write_file()
371 index1part); in genome_write_file()
380 index1part); in genome_write_file()
399 Univ_IIT_T contig_iit, char *fileroot, int index1part, in genome_writeraw_file() argument
787 Univcoord_T genomelength, int index1part, int nmessages) { in Genome_write_comp32() argument
807 /*uncompressedp*/true,index1part,nmessages); in Genome_write_comp32()
823 /*uncompressedp*/false,index1part,nmessages); in Genome_write_comp32()
[all …]
H A Dsnpindex.c112 static int index1part = 15; variable
558 nt = shortoligo_nt(oligo,index1part); in process_snp_block()
580 debug1(nt = shortoligo_nt(oligo,index1part); in process_snp_block()
592 debug1(nt = shortoligo_nt(oligo,index1part); in process_snp_block()
724 divstring,snps_iit,index1part, in write_offsets()
1001 Oligospace_T oligo, int index1part) { in merge_positions8() argument
1027 nt = shortoligo_nt(oligo,index1part); in merge_positions8()
1052 nt = shortoligo_nt(oligo,index1part); in merge_positions8()
1131 nt = shortoligo_nt(oligo,index1part); in merge_positions4()
1151 nt = shortoligo_nt(oligo,index1part); in merge_positions4()
[all …]
H A Dstage1hr.c155 static int index1part; variable
445 Oligo_one_nt(forward_oligo,index1part),Oligo_one_nt(revcomp_oligo,index1part), in Stage1_init()
513 Oligo_one_nt(forward_oligo,index1part),Oligo_one_nt(revcomp_oligo,index1part), in Stage1_init()
624 index1part+mod,this->plus_positions[index1part+mod],this->plus_npositions[index1part+mod]); in Stage1_rearrange()
626 query_lastpos-index1part-mod,this->plus_positions[query_lastpos-index1part-mod], in Stage1_rearrange()
630 index1part+mod,this->minus_positions[index1part+mod],this->minus_npositions[index1part+mod]); in Stage1_rearrange()
632 query_lastpos-index1part-mod,this->minus_positions[query_lastpos-index1part-mod], in Stage1_rearrange()
872 assert(querylength >= index1part); in determine_sizelimit()
3052 index1part = index1part_in; in Stage1hr_setup()
3071 leftreadshift = 64 - index1part - index1part; in Stage1hr_setup()
[all …]
H A Dindexdb-cat.c68 static int index1part = 15; variable
744 required_index1part = index1part; in main()
767 index1part != required_index1part || index1interval > required_index1interval) { in main()
779 index1part != required_index1part || index1interval > required_index1interval) { in main()
790 index1part = required_index1part; in main()
793 Indexdb_setup(index1part); in main()
794 oligospace = power(4,index1part); in main()
834 destdir,fileroot,IDX_FILESUFFIX,index1part,interval_char,"offsets64pages"); in main()
842 destdir,fileroot,IDX_FILESUFFIX,index1part,interval_char,"offsets64meta"); in main()
849 destdir,fileroot,IDX_FILESUFFIX,index1part,interval_char,"offsets64strm"); in main()
[all …]
H A Dextension-search.c119 static int index1part; variable
175 index1part = index1part_in; in Extension_search_setup()
180 leftreadshift = 64 - index1part - index1part; in Extension_search_setup()
183 leftreadshift = 32 - index1part - index1part; in Extension_search_setup()
383 nmatches[i] = index1part + in Elt_read_queryfwd()
385 /*pos5*/querystart+index1part,pos3, in Elt_read_queryfwd()
450 } else if (queryend < index1part) { in Elt_read_queryrev()
468 nmatches[i] = index1part + in Elt_read_queryrev()
544 nmatches[i] = index1part +
617 nmatches[i] = index1part +
[all …]
H A Datoiindex.c104 static int index1part = 15; variable
231 if (reduce_oligo(oligoi) != reduce_oligo_old(oligoi,index1part)) {
237 nt1 = shortoligo_nt(oligoi,index1part);
238 nt2 = shortoligo_nt(reduced,index1part);
282 nt1 = shortoligo_nt(oligoi,index1part);
283 nt2 = shortoligo_nt(reduced,index1part);
699 countermeta = Indexdb_bitpack_counter(&counterstrm,newoffsetsmeta,index1part); in compute_ag()
1062 if ((indexdb = Indexdb_new_genome(&index1part,&index1interval, in main()
1070 index_mask = ~(~0ULL << 2*index1part); in main()
1072 index_mask = ~(~0U << 2*index1part); in main()
[all …]
H A Dcmetindex.c104 static int index1part = 15; variable
231 if (reduce_oligo(oligoi) != reduce_oligo_old(oligoi,index1part)) {
237 nt1 = shortoligo_nt(oligoi,index1part);
238 nt2 = shortoligo_nt(reduced,index1part);
282 nt1 = shortoligo_nt(oligoi,index1part);
283 nt2 = shortoligo_nt(reduced,index1part);
839 countermeta = Indexdb_bitpack_counter(&counterstrm,newoffsetsmeta,index1part); in compute_ct()
1202 if ((indexdb = Indexdb_new_genome(&index1part,&index1interval, in main()
1210 index_mask = ~(~0ULL << 2*index1part); in main()
1212 index_mask = ~(~0U << 2*index1part); in main()
[all …]
H A Dstage1.c194 static Width_T index1part; variable
204 index1part = index1part_in; in Stage1_setup()
324 new->oligosize = index1part; in Stage1_new()
1096 matchsize = matchinterval + index1part; in identify_matches()
1188 matchinterval = matchsize - index1part; in find_5prime_matches()
1246 matchinterval = matchsize - index1part; in find_3prime_matches()
2390 /*diagterm*/querypos + index1part);
2415 /*diagterm*/querypos + index1part); in sample_oligos_nolimit()
3407 if (index1part < 12) { in scan_ends()
3408 matchsize = index1part + index1part; in scan_ends()
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H A Dterminal.c38 static int index1part = 15; variable
187 …if (first_querypos > index1part /*&& (last_querypos > query_lastpos || segment->spliceable_high_p … in find_terminals()
289 int query_lastpos = querylength - index1part; in Terminal_solve_plus()
403 int query_lastpos = querylength - index1part; in Terminal_solve_minus()
521 index1part = index1part_in; in Terminal_setup()
H A Dsegment-search.c110 static int index1part; variable
569 records[k].queryend = querypos + index1part; in make_records()
737 int query_lastpos = querylength - index1part; in Segment_identify_lower()
873 int query_lastpos = querylength - index1part; in Segment_identify_higher()
1007 int query_lastpos = querylength - index1part; in Segment_identify()
1394 index1part = index1part_in; in Segment_search_setup()
1405 leftreadshift = 64 - index1part - index1part; in Segment_search_setup()
1406 oligobase_mask = ~(~ (Oligospace_T) 0 << 2*index1part); in Segment_search_setup()
1408 leftreadshift = 32 - index1part - index1part; in Segment_search_setup()
1409 oligobase_mask = ~(~ (Oligospace_T) 0 << 2*index1part); in Segment_search_setup()
H A Dgmapindex.c104 static int index1part = 15; variable
1376 case 'k': index1part = atoi(optarg); in main()
1377 if (index1part > MAXIMUM_KMER) { in main()
1638 genomelength,index1part,nmessages); in main()
1731 noffsets = Indexdb_count_offsets(stdin,chromosome_iit,index1part,index1interval, in main()
1766 index1part,index1interval, in main()
1776 index1part,index1interval, in main()
1810 /*required_index1part*/index1part, in main()
1840 destdir,fileroot,IDX_FILESUFFIX,index1part,interval_char,POSITIONS_FILESUFFIX); in main()
1846 index1part,index1interval,genomelength, in main()
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H A Dgenome-write.h16 Univcoord_T genomelength, int index1part, int nmessages);
H A Dcompress-write.c199 int index1part) { in genomecomp_read_current() argument
202 if (fread(section,sizeof(char),index1part,fp) < (unsigned int) index1part) { in genomecomp_read_current()
346 Univcoord_T endpos, int index1part) { in Compress_update_file() argument
362 genomecomp_read_current(&high,&low,&flags,fp,index1part); in Compress_update_file()
383 genomecomp_read_current(&high,&low,&flags,fp,index1part); in Compress_update_file()
412 genomecomp_read_current(&high,&low,&flags,fp,index1part); in Compress_update_file()
H A Dcompress-write.h15 Univcoord_T endpos, int index1part);
H A Doligo.h27 Oligo_setup (int index1part, int mode);
H A Dindexdbdef.h32 Width_T index1part; member
H A Dgsnap.c375 static Width_T index1part = 15; variable
3153 if ((indexdb = Indexdb_new_genome(&index1part,&index1interval, in worker_setup()
3172 } else if ((indexdb2 = Indexdb_new_genome(&index1part,&index1interval, in worker_setup()
3234 if (min_distantsplicing_end_matches < index1part) { in worker_setup()
3440 index1part,index1interval,local1part,region1part); in worker_setup()
3448 index1part,index1interval,local1part); in worker_setup()
3452 splicingp,index1part,index1interval,subopt_levels); in worker_setup()
3454 index1part,index1interval,subopt_levels,shortsplicedist, in worker_setup()
3479 Indexdb_setup(index1part); in worker_setup()
3480 Oligo_setup(index1part,mode); in worker_setup()
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H A Doligo.c403 Oligo_setup (int index1part, int mode) { in Oligo_setup() argument
404 oligosize = index1part; in Oligo_setup()
H A Ddistant-rna.c48 static int index1part = 15; variable
411 debug4e(printf("Comparing elt->qstart %d > index1part %d\n",elt->qstart,index1part)); in find_spliceends_rna_plus()
412 …if (elt->qstart > index1part /*&& (elt->qend > query_lastpos || segment->spliceable_high_p == true… in find_spliceends_rna_plus()
929 debug4e(printf("Comparing elt->qstart %d > index1part %d\n",elt->qstart,index1part)); in find_spliceends_rna_minus()
930 …if (elt->qstart > index1part /*&& (elt->qend > query_lastpos || segment->spliceable_high_p == true… in find_spliceends_rna_minus()
1946 int query_lastpos = querylength - index1part; in Distant_rna_solve()
2098 index1part = index1part_in; in Distant_rna_setup()
H A Dkmer-search.c197 static int index1part; variable
6330 adj = (querylength - index1part) % index1interval; in Kmer_search_genome_ends_exact()
6656 /*plusp*/true,genestrand,/*query_unk_mismatch_local_p*/false,/*kmer*/index1part); in Kmer_search_genome_ends_approx()
6658 /*plusp*/true,genestrand,/*query_unk_mismatch_local_p*/false,/*kmer*/index1part); in Kmer_search_genome_ends_approx()
6664 /*plusp*/true,genestrand,/*query_unk_mismatch_local_p*/false,/*kmer*/index1part); in Kmer_search_genome_ends_approx()
6666 /*plusp*/true,genestrand,/*query_unk_mismatch_local_p*/false,/*kmer*/index1part); in Kmer_search_genome_ends_approx()
6875 index1part = index1part_in; in Kmer_search_setup()
6880 leftreadshift = 64 - index1part - index1part; in Kmer_search_setup()
6881 oligobase_mask = ~(~ (Oligospace_T) 0 << 2*index1part); in Kmer_search_setup()
6883 leftreadshift = 32 - index1part - index1part; in Kmer_search_setup()
[all …]
H A Dgmap.c217 static Width_T index1part; variable
4463 index1part in process_request()
5332 index1part
6842 if ((indexdb_fwd = Indexdb_new_genome(&index1part,&index1interval, in main()
6862 } else if ((indexdb_rev = Indexdb_new_genome(&index1part,&index1interval, in main()
7006 Oligo_setup(index1part,mode); in main()
7007 Indexdb_setup(index1part); in main()
7008 Stage1_setup(index1part,maxextension,maxtotallen_bound,circular_typeint); in main()

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