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Searched refs:reflist_options (Results 1 – 6 of 6) sorted by relevance

/dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-pileup/
H A Dinputfiles.c61 const char * path, uint32_t reflist_options, bool show_err ) in append_database() argument
64 rc_t rc = ReferenceList_MakeDatabase( &reflist, db, reflist_options, 0, NULL, 0 ); in append_database()
199 const char * path, uint32_t reflist_options, bool show_err ) in open_database() argument
218 rc = append_database( self, db, path, reflist_options, show_err ); in open_database()
272 const VNamelist * src, uint32_t reflist_options ) in split_input_files() argument
294 … case kptDatabase : rc = open_database( self, mgr, path, reflist_options, true ); break; in split_input_files()
310 const VNamelist * src, uint32_t reflist_options ) in discover_input_files() argument
330 rc = split_input_files( ipf, mgr, src, reflist_options ); in discover_input_files()
H A Dcmdline_cmn.c650 uint32_t reflist_options = ereferencelist_4na; in prepare_reflist() local
653 reflist_options |= ereferencelist_usePrimaryIds; in prepare_reflist()
656 reflist_options |= ereferencelist_useSecondaryIds; in prepare_reflist()
659 reflist_options |= ereferencelist_useEvidenceIds; in prepare_reflist()
661 rc = ReferenceList_MakeDatabase( &ctx->reflist, ctx->db, reflist_options, 0, NULL, 0 ); in prepare_reflist()
H A Dinputfiles.h95 const VNamelist * src, uint32_t reflist_options );
H A Dref_walker.c793 uint32_t reflist_options = ref_walker_make_reflist_options( self ); /* above */ in ref_walker_walk_ref_range() local
809 rc = ReferenceList_MakeDatabase( &ref_list, db, reflist_options, 0, NULL, 0 ); in ref_walker_walk_ref_range()
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/test/align/
H A Dpileup_estimator.cpp81 uint32_t reflist_options = ereferencelist_usePrimaryIds; in calc_coverage_sum_using_ref_iter() local
82 …rc = ReferenceList_MakeDatabase( &ref_list, db, reflist_options, 0, NULL, 0 ); /* align/reference.… in calc_coverage_sum_using_ref_iter()
168 uint32_t reflist_options = ereferencelist_usePrimaryIds; in calc_coverage_using_ref_iter() local
169 …rc = ReferenceList_MakeDatabase( &ref_list, db, reflist_options, 0, NULL, 0 ); /* align/reference.… in calc_coverage_using_ref_iter()
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/test/align/
H A Dpileup_estimator.cpp81 uint32_t reflist_options = ereferencelist_usePrimaryIds; in calc_coverage_sum_using_ref_iter() local
82 …rc = ReferenceList_MakeDatabase( &ref_list, db, reflist_options, 0, NULL, 0 ); /* align/reference.… in calc_coverage_sum_using_ref_iter()
168 uint32_t reflist_options = ereferencelist_usePrimaryIds; in calc_coverage_using_ref_iter() local
169 …rc = ReferenceList_MakeDatabase( &ref_list, db, reflist_options, 0, NULL, 0 ); /* align/reference.… in calc_coverage_using_ref_iter()