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Searched refs:TReadStore (Results 1 – 25 of 35) sorted by relevance

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/dports/biology/seqan1/seqan-1.3.1/seqan/store/
H A Dstore_all.h950 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
951 typename Value<TReadStore>::Type r;
969 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
970 typename Value<TReadStore>::Type r;
985 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
998 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
1113 typedef typename TFragmentStore::TReadStore TReadStore;
1142 typedef typename TFragmentStore::TReadStore TReadStore;
1331 typedef typename TFragmentStore::TReadStore TReadStore;
1666 typedef typename TFragmentStore::TReadStore TReadStore;
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H A Dstore_io_sam.h529 typedef typename TFragmentStore::TReadStore TReadStore; in _generatePairMatchIds() typedef
533 typedef typename Value<TReadStore>::Type TRead; in _generatePairMatchIds()
556 typename Size<TReadStore>::Type readStoreLength = length(fragStore.readStore); in _generatePairMatchIds()
712 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in _readOneAlignment()
930 typedef typename TFragmentStore::TReadStore TReadStore; in _writeAlignments() typedef
936 typedef typename Value<TReadStore>::Type TRead; in _writeAlignments()
H A Dstore_io_bam.h163 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in _readOneAlignment()
414 typedef typename TFragmentStore::TReadStore TReadStore; in _writeAlignments() typedef
420 typedef typename Value<TReadStore>::Type TRead; in _writeAlignments()
H A Dstore_io.h143 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in read()
507 typedef typename Iterator<typename TFragmentStore::TReadStore>::Type TReadIter; in read()
561 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in write()
636 typedef typename Iterator<typename TFragmentStore::TReadStore, Standard>::Type TReadIter; in write()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/store/
H A Dstore_all.h1051 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
1052 typename Value<TReadStore>::Type r;
1070 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
1071 typename Value<TReadStore>::Type r;
1086 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
1099 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
1220 typedef typename TFragmentStore::TReadStore TReadStore;
1223 typename Value<TReadStore>::Type r;
1249 typedef typename TFragmentStore::TReadStore TReadStore;
1252 typename Value<TReadStore>::Type r;
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H A Dstore_io.h176 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in read()
572 typedef typename Iterator<typename TFragmentStore::TReadStore>::Type TReadIter; in read()
645 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in write()
722 typedef typename Iterator<typename TFragmentStore::TReadStore, Standard>::Type TReadIter; in write()
1257 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in loadReads() typedef
1258 typedef typename Value<TReadStore>::Type TReadStoreElement; in loadReads()
H A Dstore_io_sam.h962 typedef typename TFragmentStore::TReadStore TReadStore;
963 typedef typename Value<TReadStore>::Type TReadStoreElement;
1021 typedef typename TFragmentStore::TReadStore TReadStore;
1022 typedef typename Value<TReadStore>::Type TReadStoreElement;
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/store/
H A Dstore_all.h1051 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
1052 typename Value<TReadStore>::Type r;
1070 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
1071 typename Value<TReadStore>::Type r;
1086 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
1099 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
1220 typedef typename TFragmentStore::TReadStore TReadStore;
1223 typename Value<TReadStore>::Type r;
1249 typedef typename TFragmentStore::TReadStore TReadStore;
1252 typename Value<TReadStore>::Type r;
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H A Dstore_io.h176 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in read()
572 typedef typename Iterator<typename TFragmentStore::TReadStore>::Type TReadIter; in read()
645 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in write()
722 typedef typename Iterator<typename TFragmentStore::TReadStore, Standard>::Type TReadIter; in write()
1257 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in loadReads() typedef
1258 typedef typename Value<TReadStore>::Type TReadStoreElement; in loadReads()
H A Dstore_io_sam.h962 typedef typename TFragmentStore::TReadStore TReadStore;
963 typedef typename Value<TReadStore>::Type TReadStoreElement;
1021 typedef typename TFragmentStore::TReadStore TReadStore;
1022 typedef typename Value<TReadStore>::Type TReadStoreElement;
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/store/
H A Dstore_all.h1051 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
1052 typename Value<TReadStore>::Type r;
1070 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
1071 typename Value<TReadStore>::Type r;
1086 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
1099 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore;
1222 typedef typename TFragmentStore::TReadStore TReadStore;
1225 typename Value<TReadStore>::Type r;
1251 typedef typename TFragmentStore::TReadStore TReadStore;
1254 typename Value<TReadStore>::Type r;
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H A Dstore_io.h176 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in read()
572 typedef typename Iterator<typename TFragmentStore::TReadStore>::Type TReadIter; in read()
645 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in write()
722 typedef typename Iterator<typename TFragmentStore::TReadStore, Standard>::Type TReadIter; in write()
1214 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in loadReads() typedef
1215 typedef typename Value<TReadStore>::Type TReadStoreElement; in loadReads()
H A Dstore_io_sam.h976 typedef typename TFragmentStore::TReadStore TReadStore;
977 typedef typename Value<TReadStore>::Type TReadStoreElement;
1035 typedef typename TFragmentStore::TReadStore TReadStore;
1036 typedef typename Value<TReadStore>::Type TReadStoreElement;
/dports/biology/seqan1/seqan-1.3.1/apps/insegt/
H A Doverlap_module.h223 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in buildTupleCountStore() typedef
224 typedef typename Value<TReadStore>::Type TReadStoreElement; in buildTupleCountStore()
425 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in buildAnnoCountStore() typedef
426 typedef typename Value<TReadStore>::Type TReadStoreElement; in buildAnnoCountStore()
614 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in normalizeAnnoCounts() typedef
615 typedef typename Size<TReadStore>::Type TReadStoreSize; in normalizeAnnoCounts()
723 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in normalizeTupleCounts() typedef
724 typedef typename Size<TReadStore>::Type TReadStoreSize; in normalizeTupleCounts()
H A Dfusion.h61 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in buildTupleCountStore_Fusion() typedef
62 typedef typename Value<TReadStore>::Type TReadStoreElement; in buildTupleCountStore_Fusion()
634 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in normalizeTupleCounts_Fusion() typedef
635 typedef typename Size<TReadStore>::Type TReadStoreSize; in normalizeTupleCounts_Fusion()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/insegt/
H A Doverlap_module.h248 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in buildTupleCountStore() typedef
249 typedef typename Value<TReadStore>::Type TReadStoreElement; in buildTupleCountStore()
450 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in buildAnnoCountStore() typedef
451 typedef typename Value<TReadStore>::Type TReadStoreElement; in buildAnnoCountStore()
639 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in normalizeAnnoCounts() typedef
640 typedef typename Size<TReadStore>::Type TReadStoreSize; in normalizeAnnoCounts()
748 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in normalizeTupleCounts() typedef
749 typedef typename Size<TReadStore>::Type TReadStoreSize; in normalizeTupleCounts()
H A Dfusion.h61 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in buildTupleCountStore_Fusion() typedef
62 typedef typename Value<TReadStore>::Type TReadStoreElement; in buildTupleCountStore_Fusion()
613 typedef typename FragmentStore<TSpec, TConfig>::TReadStore TReadStore; in normalizeTupleCounts_Fusion() typedef
614 typedef typename Size<TReadStore>::Type TReadStoreSize; in normalizeTupleCounts_Fusion()
/dports/biology/seqan1/seqan-1.3.1/apps/rabema/
H A Dverification.h253 typedef typename TFragmentStore::TReadStore TReadStore; in verifyMatchesToErrorFunctionResults() typedef
255 typedef typename Value<TReadStore>::Type TRead; in verifyMatchesToErrorFunctionResults()
262 TReadStore /*const*/ & reads = fragments.readStore; in verifyMatchesToErrorFunctionResults()
H A Dbuild_gold_standard.h474 typedef typename TFragmentStore::TReadStore TReadStore; in matchesToErrorFunction() typedef
476 typedef typename Value<TReadStore>::Type TRead; in matchesToErrorFunction()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/
H A Drazers_matepairs.h280 typedef typename TFragmentStore::TReadStore TReadStore;
283 typedef typename Value<TReadStore>::Type TRead;
323 typedef typename TFragmentStore::TReadStore TReadStore;
324 typedef typename Value<TReadStore>::Type TRead;
368 typedef typename TFragmentStore::TReadStore TReadStore;
369 typedef typename Value<TReadStore>::Type TRead;
/dports/biology/seqan1/seqan-1.3.1/apps/razers2/
H A Drazers_matepairs.h242 typedef typename TFragmentStore::TReadStore TReadStore;
245 typedef typename Value<TReadStore>::Type TRead;
281 typedef typename TFragmentStore::TReadStore TReadStore;
284 typedef typename Value<TReadStore>::Type TRead;
/dports/biology/seqan1/seqan-1.3.1/apps/rep_sep/
H A Dcolumn_scanner.h70 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in isCandidate()
H A Dassembly_parser.h90 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in parseContig()
/dports/biology/seqan1/seqan-1.3.1/apps/snp_store/
H A Dsnp_store.cpp252 typename TFragmentStore::TReadStore &tmpRs, in copyNextWindowMatchesAndReads()
683 typedef typename TFragmentStore::TReadStore TReadStore; in readMatchesFromGFF_Batch() typedef
684 typedef typename Value<TReadStore>::Type TReadStoreElement; in readMatchesFromGFF_Batch()
1123 typename Value<TReadStore>::Type r; in readMatchesFromGFF_Batch()
1185 typedef typename TFragmentStore::TReadStore TReadStore; // TReadSet in detectSNPs() typedef
1339 TReadStore tmpRs; in detectSNPs()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/
H A Dcasbar.cpp137 typename TFragmentStore::TReadStore &tmpRs, in copyNextWindowMatchesAndReads()
608 typedef typename TFragmentStore::TReadStore TReadStore; // TReadSet in detectSNPsForContig() typedef
625 TReadStore tmpRs; in detectSNPsForContig()

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