H A D | stage3.c | 586 int topens; member 5901 int topens, int tindels, int ncanonical, int nsemicanonical, int nnoncanonical, in Stage3_new() 6051 int goodness, matches, unknowns, mismatches, qopens, qindels, topens, tindels, in Stage3_new_from_pairs() local 9059 int unknowns, qopens, qindels, topens, tindels, ncanonical, nsemicanonical, nnoncanonical; in traverse_single_gap() local 12235 int nunknowns, qopens, qindels, topens, tindels; in score_alignment() local 13540 int matches, unknowns, mismatches, qopens, qindels, topens, tindels, in path_compute_dir() local 13888 int nmatches, nunknowns, nmismatches, qopens, qindels, topens, tindels, in path_compute_end5() local 14035 int nmatches, nunknowns, nmismatches, qopens, qindels, topens, tindels, in path_compute_end3() local 18855 int goodness, matches, unknowns, mismatches, qopens, qindels, topens, tindels, in Stage3_split() local
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