/dports/biology/seqan1/seqan-1.3.1/seqan/store/ |
H A D | store_all.h | 950 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; [all …]
|
H A D | store_io_sam.h | 529 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 D | store_io_bam.h | 163 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 D | store_io.h | 143 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 D | store_all.h | 1051 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; [all …]
|
H A D | store_io.h | 176 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 D | store_io_sam.h | 962 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 D | store_all.h | 1051 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; [all …]
|
H A D | store_io.h | 176 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 D | store_io_sam.h | 962 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 D | store_all.h | 1051 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; [all …]
|
H A D | store_io.h | 176 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 D | store_io_sam.h | 976 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 D | overlap_module.h | 223 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 D | fusion.h | 61 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 D | overlap_module.h | 248 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 D | fusion.h | 61 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 D | verification.h | 253 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 D | build_gold_standard.h | 474 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 D | razers_matepairs.h | 280 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 D | razers_matepairs.h | 242 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 D | column_scanner.h | 70 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in isCandidate()
|
H A D | assembly_parser.h | 90 typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement; in parseContig()
|
/dports/biology/seqan1/seqan-1.3.1/apps/snp_store/ |
H A D | snp_store.cpp | 252 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 D | casbar.cpp | 137 typename TFragmentStore::TReadStore &tmpRs, in copyNextWindowMatchesAndReads() 608 typedef typename TFragmentStore::TReadStore TReadStore; // TReadSet in detectSNPsForContig() typedef 625 TReadStore tmpRs; in detectSNPsForContig()
|