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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/bam_io/
H A Dbam_io_context.h209 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…
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H A Dbam_file.h111 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 */,
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H A Dwrite_sam.h50 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 Dbam_io_context.h209 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…
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H A Dbam_file.h111 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 */,
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H A Dwrite_sam.h50 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 Dbam_io_context.h209 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…
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H A Dbam_file.h111 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 */,
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H A Dwrite_sam.h50 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 Dname_store_cache.h57 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>
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/misc/
H A Dname_store_cache.h57 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>
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/misc/
H A Dname_store_cache.h57 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>
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/vcf_io/
H A Dvcf_io_context.h76 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 &
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H A Dread_vcf.h67 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 Dwrite_vcf.h48 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 Dvcf_io_context.h76 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 &
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H A Dread_vcf.h67 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 Dwrite_vcf.h48 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 Dvcf_io_context.h76 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 &
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H A Dwrite_vcf.h48 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 Dtest_bam_io_context.h62 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 Dname_store_cache.cpp10 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 Dname_store_cache.cpp10 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 Derror_rate_from_sam.cpp34 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 Dproject_spliced.h81 typedef seqan::StringSet<seqan::CharString> TNameStore; typedef
82 typedef seqan::NameStoreCache<TNameStore> TNameStoreCache;
89 TNameStore groupNames;

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