| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/bam_io/ |
| H A D | bam_io_context.h | 177 (TNameStoreCache*)NULL, in BamIOContext()
209 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>,
220 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>,
223 typedef TNameStoreCache Type;
231 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>,
270 template <typename TNameStore, typename TNameStoreCache>
331 inline TNameStoreCache &
334 return _referenceCast<TNameStoreCache &>(context._contigNamesCache);
338 inline TNameStoreCache const &
344 template <typename TNameStore, typename TNameStoreCache>
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| H A D | bam_file.h | 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,
273 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
277 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */,
287 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
315 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */,
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| 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
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| H A D | read_sam.h | 130 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp…
133 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
201 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp…
204 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
253 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp…
256 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/bam_io/ |
| H A D | bam_io_context.h | 177 (TNameStoreCache*)NULL, in BamIOContext()
209 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>,
220 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>,
223 typedef TNameStoreCache Type;
231 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>,
270 template <typename TNameStore, typename TNameStoreCache>
331 inline TNameStoreCache &
334 return _referenceCast<TNameStoreCache &>(context._contigNamesCache);
338 inline TNameStoreCache const &
344 template <typename TNameStore, typename TNameStoreCache>
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| H A D | bam_file.h | 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,
273 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
277 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */,
287 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
315 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */,
[all …]
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| 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
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| H A D | read_sam.h | 130 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp…
133 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
201 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp…
204 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
253 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp…
256 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/bam_io/ |
| H A D | bam_io_context.h | 177 (TNameStoreCache*)NULL, in BamIOContext()
209 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>,
220 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>,
223 typedef TNameStoreCache Type;
231 struct Member<BamIOContext<TNameStore, TNameStoreCache, TStorageSpec>,
270 template <typename TNameStore, typename TNameStoreCache>
331 inline TNameStoreCache &
334 return _referenceCast<TNameStoreCache &>(context._contigNamesCache);
338 inline TNameStoreCache const &
344 template <typename TNameStore, typename TNameStoreCache>
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| H A D | bam_file.h | 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,
274 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
278 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */,
288 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
316 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & /* context */,
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| 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
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| H A D | read_sam.h | 130 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp…
133 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
201 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp…
204 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
253 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp…
256 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
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| H A D | write_bam.h | 51 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
54 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in write() argument
238 template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
241 BamIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in write() argument
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/vcf_io/ |
| H A D | vcf_io_context.h | 77 typedef TNameStoreCache_ TNameStoreCache; typedef
95 (TNameStoreCache*)NULL, in VcfIOContext()
99 (TNameStoreCache*)NULL, in VcfIOContext()
110 (TNameStoreCache*)NULL, in VcfIOContext()
172 inline TNameStoreCache &
175 return _referenceCast<TNameStoreCache &>(context._contigNamesCache); in contigNamesCache()
179 inline TNameStoreCache const &
182 return _referenceCast<TNameStoreCache &>(context._contigNamesCache); in contigNamesCache()
211 inline TNameStoreCache &
214 return _referenceCast<TNameStoreCache &>(context._sampleNamesCache); in sampleNamesCache()
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| 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
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| 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
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/vcf_io/ |
| H A D | vcf_io_context.h | 77 typedef TNameStoreCache_ TNameStoreCache; typedef
95 (TNameStoreCache*)NULL, in VcfIOContext()
99 (TNameStoreCache*)NULL, in VcfIOContext()
110 (TNameStoreCache*)NULL, in VcfIOContext()
172 inline TNameStoreCache &
175 return _referenceCast<TNameStoreCache &>(context._contigNamesCache); in contigNamesCache()
179 inline TNameStoreCache const &
182 return _referenceCast<TNameStoreCache &>(context._contigNamesCache); in contigNamesCache()
211 inline TNameStoreCache &
214 return _referenceCast<TNameStoreCache &>(context._sampleNamesCache); in sampleNamesCache()
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| 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
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| 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
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/vcf_io/ |
| H A D | vcf_io_context.h | 77 typedef TNameStoreCache_ TNameStoreCache; typedef
95 (TNameStoreCache*)NULL, in VcfIOContext()
99 (TNameStoreCache*)NULL, in VcfIOContext()
110 (TNameStoreCache*)NULL, in VcfIOContext()
172 inline TNameStoreCache &
175 return _referenceCast<TNameStoreCache &>(context._contigNamesCache); in contigNamesCache()
179 inline TNameStoreCache const &
182 return _referenceCast<TNameStoreCache &>(context._contigNamesCache); in contigNamesCache()
211 inline TNameStoreCache &
214 return _referenceCast<TNameStoreCache &>(context._sampleNamesCache); in sampleNamesCache()
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| 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
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| H A D | read_vcf.h | 84 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp…
87 VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in readHeader() argument
148 template <typename TForwardIter, typename TNameStore, typename TNameStoreCache, typename TStorageSp…
151 VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context, in readRecord() argument
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| /dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/misc/ |
| H A D | name_store_cache.cpp | 11 typedef NameStoreCache<TNameStore> TNameStoreCache; in main() typedef
25 TNameStoreCache nameStoreCache(nameStore); in main()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/misc/ |
| H A D | name_store_cache.cpp | 11 typedef NameStoreCache<TNameStore> TNameStoreCache; in main() typedef
25 TNameStoreCache nameStoreCache(nameStore); in main()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/bam_io/ |
| H A D | test_bam_io_context.h | 63 typedef NameStoreCache<TNameStore> TNameStoreCache; in SEQAN_DEFINE_TEST() typedef
66 …BamIOContext<TNameStore, TNameStoreCache> bamIOContext(store.contigNameStore, store.contigNameStor… in SEQAN_DEFINE_TEST()
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