| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/bam/ |
| H A D | vdbfile.cpp | 68 bool CBamVDBPath::IsPlainAccession(const string& acc_or_path) in IsPlainAccession() argument
71 return !s_HasWindowsDriveLetter(acc_or_path) && in IsPlainAccession()
72 acc_or_path.find_first_of("/\\") == NPOS; in IsPlainAccession()
74 return acc_or_path.find('/') == NPOS; in IsPlainAccession()
96 bool CBamVDBPath::IsSysPath(const string& acc_or_path) in IsSysPath() argument
98 if (IsPlainAccession(acc_or_path)) { in IsSysPath()
101 if (HasSchemaPrefix(acc_or_path)) { in IsSysPath()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/sra/ |
| H A D | vdbread.cpp | 336 acc_or_path.find_first_of("/\\") == NPOS; in IsPlainAccession()
338 return acc_or_path.find('/') == NPOS; in IsPlainAccession()
373 return IsPlainAccession(acc_or_path) ? in ConvertAccOrSysPathToPOSIX()
374 acc_or_path : in ConvertAccOrSysPathToPOSIX()
375 ConvertSysPathToPOSIX(acc_or_path); in ConvertAccOrSysPathToPOSIX()
409 return acc_or_path; in Resolve()
418 if ( CDirEntry(acc_or_path).Exists() ) { in Resolve()
420 return acc_or_path; in Resolve()
755 : m_Name(acc_or_path) in CVDB()
847 const string& acc_or_path, in CVDBTable() argument
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| H A D | wgsresolver_impl.cpp | 426 static string s_ResolveAccOrPath(const CVDBMgr& mgr, const string& acc_or_path) in s_ResolveAccOrPath() argument
429 if ( CVPath::IsPlainAccession(acc_or_path) ) { in s_ResolveAccOrPath()
432 path = mgr.FindAccPath(acc_or_path); in s_ResolveAccOrPath()
434 LOG_POST_X(28, "CWGSResolver_VDB("<<acc_or_path<<"): -> "<<path); in s_ResolveAccOrPath()
438 path = acc_or_path; in s_ResolveAccOrPath()
443 path = acc_or_path; in s_ResolveAccOrPath()
453 LOG_POST_X(29, "CWGSResolver_VDB("<<acc_or_path<<"): " in s_ResolveAccOrPath()
462 void CWGSResolver_VDB::Open(const CVDBMgr& mgr, const string& acc_or_path) in Open() argument
464 string path = s_ResolveAccOrPath(mgr, acc_or_path); in Open()
481 m_WGSIndexPath = acc_or_path; in Open()
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| /dports/biology/sra-tools/sra-tools-2.11.0/tools/vdb-dump/ |
| H A D | vdb_info.c | 686 static const char * get_path_type( const VDBManager *mgr, const char * acc_or_path ) in get_path_type() argument
689 int path_type = ( VDBManagerPathType ( mgr, "%s", acc_or_path ) & ~ kptAlias ); in get_path_type()
1703 const char * acc_or_path, const char * table_name ) in vdb_info_1() argument
1710 data.acc = acc_or_path; in vdb_info_1()
1713 data.s_path_type = get_path_type( mgr, acc_or_path ); in vdb_info_1()
1728 …rc1 = resolve_accession( acc_or_path, data . path, sizeof data . path, false ); /* vdb-dump-helper… in vdb_info_1()
1743 … rc1 = resolve_cache( acc_or_path, data . cache, sizeof data . cache ); /* vdb-dump-helper.c */ in vdb_info_1()
1767 const char * acc_or_path, struct num_gen * rows ) in vdb_info() argument
1776 rc = vdb_info_print_sql_header( acc_or_path ); in vdb_info()
1813 rc = vdb_info_1( schema, format, mgr, acc, acc_or_path ); in vdb_info()
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| H A D | vdb_info.h | 41 const char * acc_or_path, struct num_gen * rows );
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| H A D | vdb-dump-fastq.h | 41 rc_t vdf_main( const p_dump_context ctx, const VDBManager * mgr, const char * acc_or_path );
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| H A D | vdb-dump-fastq.c | 65 static char * vdb_fastq_extract_run_name( const char * acc_or_path ) in vdb_fastq_extract_run_name() argument
67 char * delim = string_rchr ( acc_or_path, string_size( acc_or_path ), '/' ); in vdb_fastq_extract_run_name()
70 return string_dup_measure ( acc_or_path, NULL ); in vdb_fastq_extract_run_name()
78 static void init_fastq_ctx( const p_dump_context ctx, fastq_ctx * fctx, const char * acc_or_path ) in init_fastq_ctx() argument
80 fctx -> run_name = vdb_fastq_extract_run_name( acc_or_path ); in init_fastq_ctx()
1254 rc_t vdf_main( const p_dump_context ctx, const VDBManager * mgr, const char * acc_or_path ) in vdf_main() argument
1258 init_fastq_ctx( ctx, &fctx, acc_or_path ); in vdf_main()
1259 ctx -> path = string_dup_measure ( acc_or_path, NULL ); in vdf_main()
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| H A D | vdb-dump.c | 2341 static rc_t vdm_print_objtype( const VDBManager *mgr, const char * acc_or_path ) in vdm_print_objtype() argument
2343 int path_type = ( VDBManagerPathType ( mgr, "%s", acc_or_path ) & ~ kptAlias ); in vdm_print_objtype()
2424 const char * acc_or_path ) in vdm_main_one_obj() argument
2428 ctx->path = string_dup_measure ( acc_or_path, NULL ); in vdm_main_one_obj()
2440 vdm_print_objtype( mgr, acc_or_path ); in vdm_main_one_obj()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/sra/test/ |
| H A D | vdb_test.cpp | 600 string acc_or_path = DEFAULT_FILE; in Run() local
602 acc_or_path = args["file"].AsString(); in Run()
605 acc_or_path = args["acc"].AsString(); in Run()
608 string path = mgr.FindAccPath(acc_or_path); in Run()
609 cout << "Resolved "<<acc_or_path<<" -> "<<path<<endl; in Run()
699 CVDB db(mgr, acc_or_path); in Run()
752 csra_db = CCSraDb(mgr, acc_or_path); in Run()
755 acc_or_path); in Run()
761 acc_or_path<<": "<<exc); in Run()
763 out << "Correctly detected absent SRA acc: "<<acc_or_path in Run()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/readers/sra/ |
| H A D | vdbread.hpp | 160 static bool IsPlainAccession(const string& acc_or_path);
169 static string ConvertAccOrSysPathToPOSIX(const string& acc_or_path);
256 CVDB(const CVDBMgr& mgr, const string& acc_or_path);
293 const string& acc_or_path,
1052 string CVPath::ConvertAccOrSysPathToPOSIX(const string& acc_or_path) in ConvertAccOrSysPathToPOSIX() argument
1054 return acc_or_path; in ConvertAccOrSysPathToPOSIX()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/readers/bam/ |
| H A D | vdbfile.hpp | 71 static bool IsPlainAccession(const string& acc_or_path);
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| /dports/biology/sra-tools/sra-tools-2.11.0/tools/sra-dump/ |
| H A D | core.c | 926 static bool database_contains_table_name( const VDBManager * vmgr, const char * acc_or_path, const … in database_contains_table_name() argument
929 if ( ( vmgr != NULL ) && ( acc_or_path != NULL ) && ( tablename != NULL ) ) in database_contains_table_name()
932 rc_t rc = VDBManagerOpenDBRead( vmgr, &db, NULL, "%s", acc_or_path ); in database_contains_table_name()
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