Searched refs:sam_sparse_secondaries_p (Results 1 – 3 of 3) sorted by relevance
59 static bool sam_sparse_secondaries_p; variable105 sam_sparse_secondaries_p = sam_sparse_secondaries_p_in; in SAM_setup()423 if (sam_sparse_secondaries_p == true && (flag & NOT_PRIMARY) != 0) { in SAM_print_nomapping()649 if (sam_sparse_secondaries_p == true && (flag & NOT_PRIMARY) != 0) { in print_substrings()1117 if (sam_sparse_secondaries_p == true && (flag & NOT_PRIMARY) != 0) { in print_splice()
490 static bool sam_sparse_secondaries_p = false; variable2140 sam_sparse_secondaries_p = true; in parse_command_line()3524 … clip_overlap_p,merge_overlap_p,merge_samechr_p,sam_multiple_primaries_p,sam_sparse_secondaries_p, in worker_setup()
1170 sam_sparse_secondaries_p to omit SEQ and QUAL flags in secondary alignments