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Searched defs:chroffset (Results 1 – 25 of 43) sorted by relevance

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/dports/biology/gmap/gmap-2020-09-12/src/
H A Ddynprog.c140 get_genomic_nt (char *g_alt, int genomicpos, Univcoord_T chroffset, Univcoord_T chrhigh, in get_genomic_nt()
241 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, in Dynprog_Matrix32_print()
350 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, in Matrix3_print()
517 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, in Dynprog_Directions32_print()
1199 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in Dynprog_standard()
1727 … Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int genestrand, int dynprogindex) { in Dynprog_traceback_std()
H A Dget-genome.c579 genemap_print_exons (char *annot, Univcoord_T chroffset, Genome_T genome) { in genemap_print_exons()
625 genemap_print_sequence (char *annot, Univcoord_T chroffset, Genome_T genome) { in genemap_print_sequence()
685 genemap_print_gsequence (char *annot, Univcoord_T chroffset, Genome_T genome) { in genemap_print_gsequence()
810 Univcoord_T chroffset; in print_interval() local
917 Univcoord_T genomelength, genomicstart, chroffset; in main() local
H A Drecord.h21 Univcoord_T chroffset; member
H A Ddynprog_genome.c335 Univcoord_T chroffset, Univcoord_T chrhigh, int cdna_direction, bool watsonp) { in get_splicesite_probs()
406 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh) { in get_known_splicesites()
624 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, in bridge_intron_gap_8_intron_level()
877 int leftoffset, int rightoffset, Univcoord_T chroffset, Univcoord_T chrhigh, in bridge_intron_gap_8_site_level()
1397 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, in bridge_intron_gap_8_ud()
1497 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, in bridge_intron_gap_16_intron_level()
1750 int leftoffset, int rightoffset, Univcoord_T chroffset, Univcoord_T chrhigh, in bridge_intron_gap_16_site_level()
2270 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, in bridge_intron_gap_16_ud()
2369 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, in bridge_intron_gap_intron_level()
2471 int leftoffset, int rightoffset, Univcoord_T chroffset, Univcoord_T chrhigh, in bridge_intron_gap_site_level()
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H A Dpath-solve.c167 Path_print (T path, Univcoord_T chroffset) { in Path_print()
286 ,Univcoord_T chroffset in find_best_splice()
480 Chrnum_T chrnum, Univcoord_T chroffset, int querylength, in attach_qstart_diagonal()
1038 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in combine_into_qstart_alts()
1310 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in add_qstart_local()
1458 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, int querylength, in attach_qend_diagonal()
2031 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in combine_into_qend_alts()
2094 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in compute_qend_paths()
2290 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in add_qend_local()
2446 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in solve_via_segments_genome()
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H A Dstage3.c456 Univcoord_T chroffset; member
4993 Univcoord_T chroffset, Univcoord_T chrhigh, in fill_in_gaps()
5238 Univcoord_T chroffset, Univcoord_T chrhigh, in make_pairarray()
9048 Univcoord_T chroffset, Univcoord_T chrhigh, in traverse_single_gap()
9215 Univcoord_T chroffset, Univcoord_T chrhigh, in traverse_cdna_gap()
10288 Univcoord_T chroffset, Univcoord_T chrhigh, in extend_ending5()
11087 Univcoord_T chroffset, Univcoord_T chrhigh, in traverse_dual_break()
11652 Univcoord_T chroffset, Univcoord_T chrhigh, in build_pairs_end5()
11749 Univcoord_T chroffset, Univcoord_T chrhigh, in build_pairs_singles()
15545 Univcoord_T chroffset, Univcoord_T chrhigh, in path_trim()
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H A Ddynprog_end.c585 get_genomic_nt (char *g_alt, int genomicpos, Univcoord_T chroffset, Univcoord_T chrhigh, in get_genomic_nt()
661 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in traceback_nogaps()
738 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int genestrand, in traceback_local_8_upper()
933 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int genestrand, in traceback_local_16_upper()
1127 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int genestrand, in traceback_local_std()
1275 Univcoord_T chroffset, Univcoord_T chrhigh, in Dynprog_end5_gap()
1627 Univcoord_T chroffset, Univcoord_T chrhigh, in Dynprog_end5_splicejunction()
1889 Univcoord_T chroffset, Univcoord_T chrhigh, in Dynprog_end3_gap()
2204 Univcoord_T chroffset, Univcoord_T chrhigh, in Dynprog_end3_splicejunction()
2696 Univcoord_T chroffset, Univcoord_T chrhigh, in Dynprog_end5_known()
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H A Ddynprog_single.c108 get_genomic_nt (char *g_alt, int genomicpos, Univcoord_T chroffset, Univcoord_T chrhigh, in get_genomic_nt()
434 Univcoord_T chroffset, Univcoord_T chrhigh, in Dynprog_single_gap()
676 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int genestrand, in make_microexon_pairs_double()
895 Univcoord_T chroffset, Univcoord_T chrhigh, in Dynprog_microexon_int()
H A Dstage2.c1074 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, in score_querypos_lookback_one()
1467 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, in score_querypos_lookback_mult()
2012 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, in score_querypos_lookforward_one()
2391 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, in score_querypos_lookforward_mult()
3651 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, in align_compute_scores_lookback()
4229 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in traceback_one_snps()
4319 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, in align_compute_lookback()
4544 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, in align_compute_scores_lookforward()
4999 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, in align_compute_lookforward()
5287 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in convert_to_nucleotides()
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H A Dcigar.c664 Univcoord_T chroffset; in Cigar_length_substrings() local
1099 Univcoord_T chroffset; in print_substrings() local
1663 Univcoord_T chroffset; in print_halfdonor() local
1848 Univcoord_T chroffset; in print_halfacceptor() local
H A Ddynprog_simd.c1035 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in banded_matrix8_compare()
1080 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in banded_matrix8_compare_upper()
1125 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in banded_matrix8_compare_lower()
1179 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in banded_matrix16_compare()
1224 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in banded_matrix16_compare_upper()
1269 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in banded_matrix16_compare_lower()
2289 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in Dynprog_simd_8_nonavx2()
2964 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in Dynprog_simd_8()
4238 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in Dynprog_simd_8_upper()
5814 int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, in Dynprog_simd_16_nonavx2()
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H A Dsplicetrie.c174 Univcoord_T chroffset, Univcoord_T chrhigh, in solve_end5_aux()
454 Univcoord_T chroffset, Univcoord_T chrhigh, in solve_end3_aux()
727 Univcoord_T chroffset, Univcoord_T chrhigh, in Splicetrie_solve_end5()
794 Univcoord_T chroffset, Univcoord_T chrhigh, in Splicetrie_solve_end3()
H A Dparserange.c373 Univcoord_T *chroffset, Chrpos_T *chrlength, in Parserange_universal()
547 Univcoord_T *chroffset, Chrpos_T *chrlength, in Parserange_universal_iit()
H A Dsubstring.c246 Univcoord_T chroffset; member
1160 Compress_T query_compress, Univcoord_T left, Univcoord_T chroffset, in Substring_trim_qstart_nosplice()
1325 Univcoord_T chroffset, int sensedir) { in Substring_trimmed_qstarts()
1393 Univcoord_T chroffset, int sensedir) { in Substring_qstart_trim()
1477 Univcoord_T chroffset, Univcoord_T chrhigh, int sensedir) { in Substring_trimmed_qends()
1543 Univcoord_T chroffset, Univcoord_T chrhigh, int sensedir) { in Substring_qend_trim()
1624 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Substring_compute_nmatches()
2579 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Substring_new_alts_D()
2698 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Substring_new_alts_A()
3950 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) { in Substring_new_acceptor()
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H A Dgenome_sites.c25515 Univcoord_T chroffset, in prev_dinucleotide_position()
26286 Univcoord_T chroffset) { in Genome_sense_canonicalp()
26387 Univcoord_T chroffset) { in Genome_antisense_canonicalp()
H A Dsplicetrie_build.c388 Univcoord_T *splicesites, chroffset, chrhigh, position; in Splicetrie_retrieve_via_splicesites() local
808 Univcoord_T *splicesites, chroffset, chrhigh, position; in Splicetrie_retrieve_via_introns() local
1863 Univcoord_T chroffset, chrhigh, leftbound_obs, leftbound_max, rightbound_obs, rightbound_max; in Splicetrie_npartners() local
2871 Univcoord_T chroffset, chrhigh; in build_via_introns_size() local
3137 Univcoord_T chroffset, chrhigh; in Splicetrie_build_via_introns() local
H A Dgmapindex.c680 Univcoord_T chroffset = 0; in write_chromosome_file() local
860 Univcoord_T chroffset; in write_alt_scaffold_file() local
1022 Univcoord_T chroffset, universalpos1, universalpos2; in write_contig_file() local
H A Ddiag.c596 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp) { in Diag_compute_bounds()
903 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp) { in Diag_max_bounds()
H A Dsnpindex.c289 Univcoord_T chroffset, Genome_T genome, in process_snp_block()
651 Univcoord_T chroffset; in write_offsets() local
855 Univcoord_T chroffset; in compute_positions() local
H A Dknownsplicing.c250 Univcoord_T *splicesites, chroffset, chrhigh, position; in Knownsplicing_retrieve_via_splicesites() local
H A Dkmer-search.c451 Univcoord_T chroffset; member
495 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Path_new()
1607 Univcoord_T alignstart, alignend, chroffset, chrhigh; in search_transcriptome_complete() local
2878 Univcoord_T alignstart, alignend, chroffset, chrhigh; in search_transcriptome_ends() local
5242 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in combine_ends_plus()
5771 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in combine_ends_minus()
6321 Univcoord_T chroffset, chrhigh; in Kmer_search_genome_ends_exact() local
6493 Univcoord_T chroffset, chrhigh; in Kmer_search_genome_ends_approx() local
H A Ddynprog_cdna.c71 get_genomic_nt (char *g_alt, int genomicpos, Univcoord_T chroffset, Univcoord_T chrhigh, in get_genomic_nt()
814 Univcoord_T chroffset, Univcoord_T chrhigh, in Dynprog_cdna_gap()
H A Duintlist.c304 Uintlist_to_string_offset (T this, unsigned int chroffset) { in Uintlist_to_string_offset()
H A Duint8list.c303 Uint8list_to_string_offset (T this, UINT8 chroffset) { in Uint8list_to_string_offset()
H A Dpair.c249 Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp) { in Pair_set_genomepos()
720 char *chrstring, Univcoord_T chroffset, in print_genomic_sequence()
747 char *chrstring, Univcoord_T chroffset, in print_genomicalt_sequence()
777 Univcoord_T chroffset) { in compute_margin()
1176 Univcoord_T chroffset, Univ_IIT_T chromosome_iit, bool watsonp, in Pair_print_alignment()
1244 Univcoord_T chroffset, Univ_IIT_T chromosome_iit, bool referencealignp, in Pair_print_pathsummary()
1413 Univcoord_T chroffset, Univ_IIT_T chromosome_iit, in Pair_print_coordinates()
2189 Univcoord_T chroffset, Genome_T genome, Univ_IIT_T chromosome_iit, in Pair_print_exonsummary()
4456 bool prev_splicesitep, bool splicesitep, Univcoord_T chroffset, in splice_site_probs()
4491 Univcoord_T chroffset, bool watsonp) { in Pair_guess_cdna_direction_array()
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