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Searched refs:min_intronlength (Results 1 – 10 of 10) sorted by relevance

/dports/biology/gmap/gmap-2020-09-12/src/
H A Dindel.h46 int min_intronlength, bool want_lowest_coordinate_p);
H A Dindel.c673 int min_intronlength, bool want_lowest_coordinate_p) { in Indel_resolve_middle_deletion_or_splice() argument
729 if (-indels >= min_intronlength) { in Indel_resolve_middle_deletion_or_splice()
792 if (-indels >= min_intronlength) { in Indel_resolve_middle_deletion_or_splice()
849 if (-indels >= min_intronlength) { in Indel_resolve_middle_deletion_or_splice()
911 if (-indels >= min_intronlength) { in Indel_resolve_middle_deletion_or_splice()
968 if (-indels >= min_intronlength) { in Indel_resolve_middle_deletion_or_splice()
1022 if (-indels >= min_intronlength) { in Indel_resolve_middle_deletion_or_splice()
H A Dgsnap.c190 static int min_intronlength = 9; variable
3438 min_intronlength,novelsplicingp,splicingp, in worker_setup()
3442 min_intronlength,chromosome_iit,genomelength,circular_typeint,circularp, in worker_setup()
3447 min_intronlength,max_end_insertions,max_end_deletions, in worker_setup()
3498 min_intronlength,expected_pairlength,pairlength_deviation, in worker_setup()
H A Dpath-solve.c96 static Chrpos_T min_intronlength; variable
628 min_intronlength,/*want_lowest_coordinate_p*/true)) <= 0) { in attach_qstart_diagonal()
642 if ((Chrpos_T) nindels < min_intronlength || splicingp == false || circularp[chrnum] == true) { in attach_qstart_diagonal()
1622 min_intronlength,/*want_lowest_coordinate_p*/true)) <= 0) { in attach_qend_diagonal()
1636 if ((Chrpos_T) nindels < min_intronlength || splicingp == false || circularp[chrnum] == true) { in attach_qend_diagonal()
4026 min_intronlength = min_intronlength_in; in Path_solve_setup()
H A Dextension-search.c115 static Chrpos_T min_intronlength; variable
171 min_intronlength = min_intronlength_in; in Extension_search_setup()
H A Dkmer-search.c194 static Chrpos_T min_intronlength; variable
5431 genestrand,min_intronlength,/*want_lowest_coordinate_p*/true)) <= 0) { in combine_ends_plus()
5443 } else if ((Chrpos_T) (nindels = adj) < min_intronlength) { in combine_ends_plus()
5960 genestrand,min_intronlength,/*want_lowest_coordinate_p*/true)) <= 0) { in combine_ends_minus()
5972 } else if ((Chrpos_T) (nindels = adj) < min_intronlength) { in combine_ends_minus()
6891 min_intronlength = min_intronlength_in; in Kmer_search_setup()
H A Dstage3.c333 static int min_intronlength; variable
394 min_intronlength = min_intronlength_in; in Stage3_setup()
1846 if (intronlength < min_intronlength) { in assign_gap_types()
2112 if (intronlength < min_intronlength) { in assign_intron_probs()
2362 if (intronlength < min_intronlength) { in remove_indel_gaps()
2603 if (intronlength < min_intronlength) { in add_intron()
2633 if (intronlength < min_intronlength) { in add_intron()
5087 } else if (intronlength < min_intronlength) { in fill_in_gaps()
5089 intronlength,min_intronlength)); in fill_in_gaps()
18677 if (intronlength >= min_intronlength && splicingp == true) { in Stage3_merge_local()
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H A Dgmap.c345 static int min_intronlength = 9; variable
5764 min_intronlength = atoi(check_valid_int(optarg)); in parse_command_line()
7028 min_intronlength,max_deletionlength,/*min_indel_end_matches*/6, in main()
7415 ",min_intronlength); in print_program_usage()
H A Dstage1hr.c199 static Chrpos_T min_intronlength; variable
3097 min_intronlength = min_intronlength_in; in Stage1hr_setup()
/dports/biology/gmap/gmap-2020-09-12/
H A DChangeLog3168 min_intronlength and max_deletionlen to see if they are introns
10339 * gsnap.c, stage1hr.c, stage1hr.h, uniqscan.c: Using min_intronlength to
12538 * stage3.c, stage3.h, gmap.c, gsnap.c: Added parameter for min_intronlength