| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/ |
| H A D | razers.cpp | 117 CharString & errorPrbFileName, in mapReads() argument
232 …meFileNames, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); in mapReads()
420 RazerSOptions<> & options, ParamChooserOptions & pm_options, CharString &errorPrbFileName, in extractOptions() argument
480 getOptionValue(errorPrbFileName, parser, "error-distr"); in extractOptions()
591 CharString errorPrbFileName; in main() local
610 …res = extractOptions(genomeFileNames, readFileNames, options, pm_options, errorPrbFileName, argPar… in main()
697 int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); in main()
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| H A D | outputFormat.h | 524 CharString errorPrbFileName, in dumpMatches() argument
570 …ns.outputFormat == 0 && !options.hammingOnly) || options.dumpAlignment || !empty(errorPrbFileName)) in dumpMatches()
1216 if (!empty(errorPrbFileName) && maxReadLength > 0) in dumpMatches()
1219 file.open(toCString(errorPrbFileName), ::std::ios_base::out | ::std::ios_base::trunc); in dumpMatches()
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| /dports/biology/seqan1/seqan-1.3.1/apps/razers2/ |
| H A D | razers.cpp | 121 CharString & errorPrbFileName, in mapReads() argument
234 …dumpMatches(store, genomeFileNames, gnoToFileMap, stats, readFileNames[0], errorPrbFileName, optio… in mapReads()
253 CharString errorPrbFileName; in main() local
379 getOptionValueLong(parser, "error-distr", errorPrbFileName); in main()
566 int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); in main()
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| H A D | outputFormat.h | 542 CharString errorPrbFileName, in dumpMatches() argument
590 …umpAlignment || options.outputFormat == 4 || options.outputFormat == 5 || !empty(errorPrbFileName)) in dumpMatches()
1181 if (!empty(errorPrbFileName) && maxReadLength > 0) in dumpMatches()
1183 file.open(toCString(errorPrbFileName), std::ios_base::out | std::ios_base::trunc); in dumpMatches()
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| /dports/biology/seqan1/seqan-1.3.1/apps/razers/ |
| H A D | razers.cpp | 127 CharString & errorPrbFileName, in mapReads() argument
243 …meFileNames, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); in mapReads()
262 CharString errorPrbFileName; in main() local
397 getOptionValueLong(parser, "error-distr", errorPrbFileName); in main()
610 int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); in main()
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| H A D | outputFormat.h | 518 CharString errorPrbFileName, in dumpMatches() argument
564 …ns.outputFormat == 0 && !options.hammingOnly) || options.dumpAlignment || !empty(errorPrbFileName)) in dumpMatches()
1206 if (!empty(errorPrbFileName) && maxReadLength > 0) in dumpMatches()
1208 file.open(toCString(errorPrbFileName), ::std::ios_base::out | ::std::ios_base::trunc); in dumpMatches()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/micro_razers/ |
| H A D | micro_razers.cpp | 93 CharString errorPrbFileName, in mapMicroRNAReads() argument
184 …ileNameList, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); in mapMicroRNAReads()
204 CharString errorPrbFileName; in main() local
551 int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); in main()
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| H A D | outputFormat.h | 302 CharString errorPrbFileName, in dumpMatches() argument
326 …ns.outputFormat == 0 && !options.hammingOnly) || options.dumpAlignment || !empty(errorPrbFileName)) in dumpMatches()
562 if (!empty(errorPrbFileName) && maxReadLength > 0) in dumpMatches()
565 file.open(toCString(errorPrbFileName), ::std::ios_base::out | ::std::ios_base::trunc); in dumpMatches()
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| /dports/biology/seqan1/seqan-1.3.1/apps/splazers/ |
| H A D | splazers.cpp | 125 CharString & errorPrbFileName, in mapReads() argument
253 …meFileNames, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); in mapReads()
272 CharString errorPrbFileName; in main() local
415 getOptionValueLong(parser, "error-distr", errorPrbFileName); in main()
651 int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); in main()
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| H A D | outputFormat.h | 625 CharString errorPrbFileName, in dumpMatches() argument
673 …at == 0 && !options.hammingOnly) || options.dumpAlignment || !empty(errorPrbFileName) || options.o… in dumpMatches()
1500 if (!empty(errorPrbFileName) && maxReadLength > 0) in dumpMatches()
1502 file.open(toCString(errorPrbFileName), ::std::ios_base::out | ::std::ios_base::trunc); in dumpMatches()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/splazers/ |
| H A D | splazers.cpp | 115 CharString & errorPrbFileName, in mapReads() argument
281 …gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); in mapReads()
295 CharString errorPrbFileName; in main() local
510 getOptionValue(errorPrbFileName, parser, "error-distr"); in main()
717 int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); in main()
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| H A D | outputFormat.h | 704 CharString errorPrbFileName, in dumpMatches() argument
755 …at == 0 && !options.hammingOnly) || options.dumpAlignment || !empty(errorPrbFileName) || options.o… in dumpMatches()
1843 if (!empty(errorPrbFileName) && maxReadLength > 0) in dumpMatches()
1846 file.open(toCString(errorPrbFileName), ::std::ios_base::out | ::std::ios_base::trunc); in dumpMatches()
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| /dports/biology/seqan1/seqan-1.3.1/apps/micro_razers/ |
| H A D | micro_razers.cpp | 91 const char *errorPrbFileName, in mapMicroRNAReads() argument
184 …ileNameList, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); in mapMicroRNAReads()
262 string errorPrbFileName; in main() local
660 int result = mapMicroRNAReads(fname[0], fname + 1, errorPrbFileName.c_str(), options); in main()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/ |
| H A D | outputFormat.h | 523 …ns.outputFormat == 4 || options.outputFormat == 5 || !empty(options.errorPrbFileName) || !empty(op… in dumpMatches()
1230 …ment || options.outputFormat == 4 || options.outputFormat == 5 || !empty(options.errorPrbFileName)) in dumpMatches()
1245 if (!empty(options.errorPrbFileName) && maxReadLength > 0) in dumpMatches()
1248 file.open(toCString(options.errorPrbFileName), std::ios_base::out | std::ios_base::trunc); in dumpMatches()
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| H A D | razers.cpp | 596 getOptionValue(options.errorPrbFileName, parser, "error-distr"); in extractOptions()
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| H A D | razers.h | 233 CharString errorPrbFileName; member
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| /dports/biology/seqan1/seqan-1.3.1/apps/snp_store/ |
| H A D | snp_store.h | 145 const char *errorPrbFileName; // name of result file
254 errorPrbFileName = "";
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