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Searched defs:chrlength (Results 1 – 24 of 24) sorted by relevance

/dports/biology/gmap/gmap-2020-09-12/src/
H A Drecord.h23 Chrpos_T chrlength; member
H A Diit_dump.c128 unsigned int divlength, chrlength, low, high, lastpos, pos; in print_runlengths() local
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 Dpath-solve.c1038 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in combine_into_qstart_alts()
1102 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in compute_qstart_paths()
1310 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in add_qstart_local()
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()
3197 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in compute_qstart_local()
3325 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in compute_qend_local()
3456 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Path_solve_from_diagonals()
H A Dsplicetrie_build.c389 Chrpos_T chrlength, chrpos; in Splicetrie_retrieve_via_splicesites() local
809 Chrpos_T chrlength, chrpos; in Splicetrie_retrieve_via_introns() local
1865 Chrpos_T chrlength; in Splicetrie_npartners() local
2872 Chrpos_T chrlength; in build_via_introns_size() local
3138 Chrpos_T chrlength; in Splicetrie_build_via_introns() local
H A Dsubstring.c248 Chrpos_T chrlength; member
328 Chrpos_T chrlength; in Substring_alias_circular() local
373 Chrpos_T chrlength; in Substring_unalias_circular() local
1624 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Substring_compute_nmatches()
1827 …_T query_compress, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Substring_new()
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()
3907 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) { in Substring_new_donor()
3950 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) { in Substring_new_acceptor()
4030 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) { in Substring_new_startfrag()
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H A Dknownsplicing.c251 Chrpos_T chrlength, chrpos; in Knownsplicing_retrieve_via_splicesites() local
H A Dkmer-search.c453 Chrpos_T chrlength; member
495 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Path_new()
1606 Chrpos_T *exonstarts, genomicpos, chrlength; in search_transcriptome_complete() local
2877 Chrpos_T *exonstarts, genomicpos, chrlength; 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()
6320 Chrpos_T chrlength; in Kmer_search_genome_ends_exact() local
6492 Chrpos_T chrlength; in Kmer_search_genome_ends_approx() local
H A Ddistant-rna.c170 Chrpos_T chrlength; in find_spliceends_rna_plus() local
686 Chrpos_T chrlength; in find_spliceends_rna_minus() local
H A Dterminal.c85 Chrpos_T chrlength; in find_terminals() local
H A Dgmap.c1151 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in update_stage3middle_list()
1255 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in update_stage3list()
1465 Chrpos_T chrlength, chrpos; in stage3_from_usersegment() local
1779 Chrpos_T chrlength; in stage3_from_gregions() local
1982 Chrpos_T *chrlength, bool *plusp, int *genestrand, in middle_piece_local_p()
3633 Chrpos_T chrstart, chrend, chrlength; in check_middle_piece_local() local
4071 Chrpos_T chrlength; in apply_stage3() local
H A Dstage3hr.c3522 Chrpos_T chrlength; in Stage3end_new_terminal() local
3720 … int querylength, Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Stage3end_new_precomputed()
3969 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Stage3end_nmatches_substrings()
4310 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Stage3end_new_substrings()
4992 Chrpos_T chrlength, Listpool_T listpool, Method_T method, int level) { in Stage3end_new_substitution()
7391 Chrpos_T chrlength = hit->chrlength; in unalias_circular() local
7490 normalize_coord (Univcoord_T orig, int circularalias, Chrpos_T chrlength) { in normalize_coord()
11281 Chrpos_T chrlength = hit->chrlength; in alias_circular() local
15016 Chrpos_T chrlength; in Stage3end_linearize_5() local
15050 Chrpos_T chrlength; in Stage3end_linearize_3() local
H A Dsnpindex.c652 Chrpos_T chrlength; in write_offsets() local
856 Chrpos_T chrlength; in compute_positions() local
H A Dextension-search.c1394 Chrpos_T *chrlength, List_T *sense_hits, List_T *antisense_hits, in process_seed()
1600 Chrpos_T chrlength; in extend_seeds() local
H A Dsimplepair.c1532 Chrpos_T chrpos, Chrpos_T chrlength, in print_overlap_sam_line()
1735 int absmq_score, int second_absmq, Chrpos_T chrpos, Chrpos_T chrlength, in Simplepair_overlap_print_sam()
H A Diit-read-univ.c266 Chrpos_T genomiclength, chrstart, chrend, chrlength; in Univ_IIT_altlocp() local
2126 …v_IIT_update_chrnum (int *chrnum, Univcoord_T *chroffset, Univcoord_T chrhigh, Chrpos_T *chrlength, in Univ_IIT_update_chrnum()
2245 Univ_IIT_get_chrnum (Univcoord_T *chroffset, Univcoord_T *chrhigh, Chrpos_T *chrlength, in Univ_IIT_get_chrnum()
H A Dpair.c3800 Pair_circularpos (int *alias, struct T *pairs, int npairs, Chrpos_T chrlength, bool plusp, int quer… in Pair_circularpos()
5066 Pair_alias_circular (struct T *pairs, int npairs, Chrpos_T chrlength) { in Pair_alias_circular()
5083 Pair_unalias_circular (struct T *pairs, int npairs, Chrpos_T chrlength) { in Pair_unalias_circular()
5851 Univ_IIT_T chromosome_iit, Chrpos_T chrpos, Chrpos_T chrlength, in print_sam_line()
6334 int absmq_score, int second_absmq, Chrpos_T chrpos, Chrpos_T chrlength, in Pair_print_sam()
7068 int npairs, bool watsonp, Chrpos_T chrlength) { in count_psl_blocks_pro()
7342 Chrpos_T chrlength; in Pair_print_pslformat_pro() local
9540 Chrpos_T chrlength, int wraplength, bool include_utr_p) { in Pair_print_mask_introns()
10487 Chrpos_T chrlength, Pairpool_T pairpool, bool plusp) { in Pair_split_circular()
H A Dstage3hrdef.h84 Chrpos_T chrlength; member
H A Dget-genome.c918 Chrpos_T genomiclength, chrlength, chrstart, chrend; in main() local
H A Dgmapindex.c681 Chrpos_T chrlength, alt_scaffold_start, alt_scaffold_end; in write_chromosome_file() local
H A Dsegment-search.c508 Chrpos_T chrlength; in make_records() local
H A Dgregion.c72 Chrpos_T chrlength; member
H A Dgenome.c10575 Chrpos_T chrlength; in fill_buffer() local
H A Dstage3.c458 Chrpos_T chrlength; member
506 Chrpos_T chrlength, bool watsonp, int genestrand, in Stage3middle_new()
569 Chrpos_T chrlength; member
5902 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Stage3_new()
6048 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) { in Stage3_new_from_pairs()
15690 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength, in Stage3_compute_middle()