/dports/biology/seqan/seqan-library-2.4.0/include/seqan/bam_io/ |
H A D | bam_io_context.h | 209 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>, 212 typedef TNameStore Type; 220 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>, 231 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>, 257 inline TNameStore & 260 return _referenceCast<TNameStore &>(context._contigNames); 264 inline TNameStore const & 267 return _referenceCast<TNameStore const &>(context._contigNames); 270 template <typename TNameStore, typename TNameStoreCache> 272 setContigNames(BamIOContext<TNameStore, TNameStoreCache, Dependent<> > & context, TNameStore & cont… [all …]
|
H A D | bam_file.h | 111 typedef StringSet<CharString> TNameStore; 112 typedef NameStoreCache<TNameStore> TNameStoreCache; 113 typedef BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> Type; 152 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */, 162 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, 214 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */, 224 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, 277 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */, 287 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, 315 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */, [all …]
|
H A D | write_sam.h | 50 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 53 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & /*context*/, in write() argument 82 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 85 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context, in write() argument 125 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 128 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context, in write() argument
|
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/bam_io/ |
H A D | bam_io_context.h | 209 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>, 212 typedef TNameStore Type; 220 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>, 231 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>, 257 inline TNameStore & 260 return _referenceCast<TNameStore &>(context._contigNames); 264 inline TNameStore const & 267 return _referenceCast<TNameStore const &>(context._contigNames); 270 template <typename TNameStore, typename TNameStoreCache> 272 setContigNames(BamIOContext<TNameStore, TNameStoreCache, Dependent<> > & context, TNameStore & cont… [all …]
|
H A D | bam_file.h | 111 typedef StringSet<CharString> TNameStore; 112 typedef NameStoreCache<TNameStore> TNameStoreCache; 113 typedef BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> Type; 152 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */, 162 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, 214 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */, 224 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, 277 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */, 287 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, 315 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */, [all …]
|
H A D | write_sam.h | 50 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 53 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & /*context*/, in write() argument 82 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 85 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context, in write() argument 125 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 128 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context, in write() argument
|
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/bam_io/ |
H A D | bam_io_context.h | 209 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>, 212 typedef TNameStore Type; 220 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>, 231 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>, 257 inline TNameStore & 260 return _referenceCast<TNameStore &>(context._contigNames); 264 inline TNameStore const & 267 return _referenceCast<TNameStore const &>(context._contigNames); 270 template <typename TNameStore, typename TNameStoreCache> 272 setContigNames(BamIOContext<TNameStore, TNameStoreCache, Dependent<> > & context, TNameStore & cont… [all …]
|
H A D | bam_file.h | 111 typedef StringSet<CharString> TNameStore; 112 typedef NameStoreCache<TNameStore> TNameStoreCache; 113 typedef BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> Type; 152 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */, 162 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, 214 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */, 224 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, 278 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */, 288 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, 316 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */, [all …]
|
H A D | write_sam.h | 50 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 53 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & /*context*/, in write() argument 82 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 85 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context, in write() argument 125 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 128 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> const & context, in write() argument
|
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/misc/ |
H A D | name_store_cache.h | 57 template <typename TNameStore, typename TName> 62 TNameStore *nameStore; 144 template <typename TNameStore, typename TName = String<typename Value<typename Value<TNameStore>::T… 159 NameStoreCache(TNameStore & nameStore): in NameStoreCache() 186 template <typename TNameStore, typename TName> 187 inline TNameStore & 193 template <typename TNameStore, typename TName> 194 inline TNameStore & 213 template <typename TNameStore, typename TName> 235 template <typename TNameStore, typename TName> [all …]
|
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/misc/ |
H A D | name_store_cache.h | 57 template <typename TNameStore, typename TName> 62 TNameStore *nameStore; 144 template <typename TNameStore, typename TName = String<typename Value<typename Value<TNameStore>::T… 159 NameStoreCache(TNameStore & nameStore): in NameStoreCache() 186 template <typename TNameStore, typename TName> 187 inline TNameStore & 193 template <typename TNameStore, typename TName> 194 inline TNameStore & 213 template <typename TNameStore, typename TName> 235 template <typename TNameStore, typename TName> [all …]
|
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/misc/ |
H A D | name_store_cache.h | 57 template <typename TNameStore, typename TName> 62 TNameStore *nameStore; 144 template <typename TNameStore, typename TName = String<typename Value<typename Value<TNameStore>::T… 159 NameStoreCache(TNameStore & nameStore): in NameStoreCache() 186 template <typename TNameStore, typename TName> 187 inline TNameStore & 193 template <typename TNameStore, typename TName> 194 inline TNameStore & 213 template <typename TNameStore, typename TName> 235 template <typename TNameStore, typename TName> [all …]
|
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/vcf_io/ |
H A D | vcf_io_context.h | 76 typedef TNameStore_ TNameStore; typedef 103 VcfIOContext(TNameStore & nameStore_, TNameStoreCache & nameStoreCache_) : in VcfIOContext() 147 inline TNameStore & 148 contigNames(VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context) in contigNames() argument 150 return _referenceCast<TNameStore &>(context._contigNames); in contigNames() 154 inline TNameStore const & 157 return _referenceCast<TNameStore &>(context._contigNames); in contigNames() 197 inline TNameStore & 200 return _referenceCast<TNameStore &>(context._sampleNames); in sampleNames() 204 inline TNameStore const & [all …]
|
H A D | read_vcf.h | 67 template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec, typename TString> 69 _readVcfContig(VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, TString const & h… in _readVcfContig() argument 101 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp… 104 VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in readHeader() argument 166 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp… 169 VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in readRecord() argument
|
H A D | write_vcf.h | 48 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 52 VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in writeHeader() argument 77 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 81 VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in writeRecord() argument
|
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/vcf_io/ |
H A D | vcf_io_context.h | 76 typedef TNameStore_ TNameStore; typedef 103 VcfIOContext(TNameStore & nameStore_, TNameStoreCache & nameStoreCache_) : in VcfIOContext() 147 inline TNameStore & 148 contigNames(VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context) in contigNames() argument 150 return _referenceCast<TNameStore &>(context._contigNames); in contigNames() 154 inline TNameStore const & 157 return _referenceCast<TNameStore &>(context._contigNames); in contigNames() 197 inline TNameStore & 200 return _referenceCast<TNameStore &>(context._sampleNames); in sampleNames() 204 inline TNameStore const & [all …]
|
H A D | read_vcf.h | 67 template <typename TNameStore, typename TNameStoreCache, typename TStorageSpec, typename TString> 69 _readVcfContig(VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, TString const & h… in _readVcfContig() argument 101 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp… 104 VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in readHeader() argument 166 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp… 169 VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in readRecord() argument
|
H A D | write_vcf.h | 48 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 52 VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in writeHeader() argument 77 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 81 VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in writeRecord() argument
|
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/vcf_io/ |
H A D | vcf_io_context.h | 76 typedef TNameStore_ TNameStore; typedef 103 VcfIOContext(TNameStore & nameStore_, TNameStoreCache & nameStoreCache_) : in VcfIOContext() 147 inline TNameStore & 148 contigNames(VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context) in contigNames() argument 150 return _referenceCast<TNameStore &>(context._contigNames); in contigNames() 154 inline TNameStore const & 157 return _referenceCast<TNameStore &>(context._contigNames); in contigNames() 197 inline TNameStore & 200 return _referenceCast<TNameStore &>(context._sampleNames); in sampleNames() 204 inline TNameStore const & [all …]
|
H A D | write_vcf.h | 48 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 52 VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in writeHeader() argument 77 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec> 81 VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in writeRecord() argument
|
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/bam_io/ |
H A D | test_bam_io_context.h | 62 typedef typename FragmentStore<>::TNameStore TNameStore; in SEQAN_DEFINE_TEST() typedef 63 typedef NameStoreCache<TNameStore> TNameStoreCache; in SEQAN_DEFINE_TEST() 66 …BamIOContext<TNameStore, TNameStoreCache> bamIOContext(store.contigNameStore, store.contigNameStor… in SEQAN_DEFINE_TEST()
|
/dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/misc/ |
H A D | name_store_cache.cpp | 10 typedef StringSet<CharString> TNameStore; in main() typedef 11 typedef NameStoreCache<TNameStore> TNameStoreCache; in main() 18 TNameStore nameStore; in main()
|
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/misc/ |
H A D | name_store_cache.cpp | 10 typedef StringSet<CharString> TNameStore; in main() typedef 11 typedef NameStoreCache<TNameStore> TNameStoreCache; in main() 18 TNameStore nameStore; in main()
|
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/fiona/ |
H A D | error_rate_from_sam.cpp | 34 typedef StringSet<CharString> TNameStore; in main() typedef 35 typedef NameStoreCache<TNameStore> TNameStoreCache; in main() 37 TNameStore refNameStore; in main() 39 BamIOContext<TNameStore> context(refNameStore, refNameStoreCache); in main()
|
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/ngs_roi/ |
H A D | project_spliced.h | 81 typedef seqan::StringSet<seqan::CharString> TNameStore; typedef 82 typedef seqan::NameStoreCache<TNameStore> TNameStoreCache; 89 TNameStore groupNames;
|