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[(Rfn.ShortReadQ,DNAStringSet,QualityScore,missing.Rdash.method) (Rfn.ShortReadQA.Rdash.class.1)] >> endobj 2212 0 obj << /Names [(Rfn.ShortReadQQA.Rdash.class) 440 0 R (Rfn.SolexaExportQA) 1041 0 R (Rfn.SolexaExportQA.Rdash.class) 1036 0 R (Rfn.SolexaExportQA.Rdash.class.1) 106 0 R (Rfn.SolexaIntensity) 479 0 R (Rfn.SolexaIntensity.1) 114 0 R] /Limits [(Rfn.ShortReadQQA.Rdash.class) (Rfn.SolexaIntensity.1)] >> endobj 2213 0 obj << /Names [(Rfn.SolexaIntensity.Rdash.class) 478 0 R (Rfn.SolexaIntensity.Rdash.class.1) 110 0 R (Rfn.SolexaIntensityInfo) 1096 0 R (Rfn.SolexaIntensityInfo.Rdash.class) 1058 0 R (Rfn.SolexaPath) 1120 0 R (Rfn.SolexaPath.Rdash.class) 421 0 R] /Limits [(Rfn.SolexaIntensity.Rdash.class) (Rfn.SolexaPath.Rdash.class)] >> endobj 2214 0 obj << /Names [(Rfn.SolexaPath.Rdash.class.1) 118 0 R (Rfn.SolexaRealignQA.Rdash.class) 1042 0 R (Rfn.SolexaSet) 1159 0 R (Rfn.SolexaSet,SolexaPath.Rdash.method) 1121 0 R (Rfn.SolexaSet,character.Rdash.method) 1160 0 R (Rfn.SolexaSet.Rdash.class) 1153 0 R] /Limits [(Rfn.SolexaPath.Rdash.class.1) (Rfn.SolexaSet.Rdash.class)] >> endobj 2215 0 obj << /Names [(Rfn.SolexaSet.Rdash.class.1) 122 0 R (Rfn.Utilites) 1300 0 R (Rfn.Utilites.1) 154 0 R (Rfn.Versioned) 260 0 R (Rfn.XStringSet) 1214 0 R (Rfn.[,AlignedRead,ANY,ANY,ANY.Rdash.method) 293 0 R] /Limits [(Rfn.SolexaSet.Rdash.class.1) (Rfn.[,AlignedRead,ANY,ANY,ANY.Rdash.method)] >> endobj 2216 0 obj << /Names [(Rfn.[,AlignedRead,ANY,ANY.Rdash.method) 294 0 R (Rfn.[,AlignedRead,ANY,missing,ANY.Rdash.method) 295 0 R (Rfn.[,AlignedRead,ANY,missing.Rdash.method) 296 0 R (Rfn.[,AlignedRead,missing,ANY,ANY.Rdash.method) 297 0 R (Rfn.[,AlignedRead,missing,ANY.Rdash.method) 298 0 R (Rfn.[,AlignedRead,missing,missing,ANY.Rdash.method) 299 0 R] /Limits [(Rfn.[,AlignedRead,ANY,ANY.Rdash.method) (Rfn.[,AlignedRead,missing,missing,ANY.Rdash.method)] >> endobj 2217 0 obj << /Names [(Rfn.[,AlignedRead,missing,missing.Rdash.method) 300 0 R (Rfn.[,IntensityMeasure,ANY,ANY,ANY.Rdash.method) 467 0 R (Rfn.[,IntensityMeasure,ANY,ANY.Rdash.method) 468 0 R (Rfn.[,IntensityMeasure,ANY,missing,ANY.Rdash.method) 469 0 R (Rfn.[,IntensityMeasure,missing,ANY,ANY.Rdash.method) 470 0 R (Rfn.[,IntensityMeasure,missing,missing,ANY.Rdash.method) 471 0 R] /Limits [(Rfn.[,AlignedRead,missing,missing.Rdash.method) (Rfn.[,IntensityMeasure,missing,missing,ANY.Rdash.method)] >> endobj 2218 0 obj << /Names [(Rfn.[,MatrixQuality,ANY,missing,ANY.Rdash.method) 564 0 R (Rfn.[,MatrixQuality,ANY,missing.Rdash.method) 565 0 R (Rfn.[,QualityScore,ANY,missing,ANY.Rdash.method) 566 0 R (Rfn.[,QualityScore,ANY,missing.Rdash.method) 567 0 R (Rfn.[,SRList,ANY,missing,ANY.Rdash.method) 853 0 R (Rfn.[,SRList,ANY,missing.Rdash.method) 854 0 R] /Limits [(Rfn.[,MatrixQuality,ANY,missing,ANY.Rdash.method) (Rfn.[,SRList,ANY,missing.Rdash.method)] >> endobj 2219 0 obj << /Names [(Rfn.[,ShortRead,ANY,ANY,ANY.Rdash.method) 920 0 R (Rfn.[,ShortRead,ANY,ANY.Rdash.method) 921 0 R (Rfn.[,ShortRead,ANY,missing,ANY.Rdash.method) 922 0 R (Rfn.[,ShortRead,ANY,missing.Rdash.method) 923 0 R (Rfn.[,ShortRead,missing,ANY,ANY.Rdash.method) 924 0 R (Rfn.[,ShortRead,missing,ANY.Rdash.method) 925 0 R] /Limits [(Rfn.[,ShortRead,ANY,ANY,ANY.Rdash.method) (Rfn.[,ShortRead,missing,ANY.Rdash.method)] >> endobj 2220 0 obj << /Names [(Rfn.[,ShortRead,missing,missing,ANY.Rdash.method) 926 0 R (Rfn.[,ShortRead,missing,missing.Rdash.method) 927 0 R (Rfn.[,ShortReadQ,ANY,ANY,ANY.Rdash.method) 996 0 R (Rfn.[,ShortReadQ,ANY,ANY.Rdash.method) 997 0 R (Rfn.[,ShortReadQ,ANY,missing,ANY.Rdash.method) 998 0 R (Rfn.[,ShortReadQ,ANY,missing.Rdash.method) 999 0 R] /Limits [(Rfn.[,ShortRead,missing,missing,ANY.Rdash.method) (Rfn.[,ShortReadQ,ANY,missing.Rdash.method)] >> endobj 2221 0 obj << /Names [(Rfn.[,ShortReadQ,missing,ANY,ANY.Rdash.method) 1000 0 R (Rfn.[,ShortReadQ,missing,ANY.Rdash.method) 1001 0 R (Rfn.[,ShortReadQ,missing,missing,ANY.Rdash.method) 1002 0 R (Rfn.[,ShortReadQ,missing,missing.Rdash.method) 1003 0 R (Rfn.[,SolexaIntensity,ANY,ANY,ANY.Rdash.method) 1059 0 R (Rfn.[,SolexaIntensity,ANY,ANY.Rdash.method) 1060 0 R] /Limits [(Rfn.[,ShortReadQ,missing,ANY,ANY.Rdash.method) (Rfn.[,SolexaIntensity,ANY,ANY.Rdash.method)] >> endobj 2222 0 obj << /Names [(Rfn.[,SolexaIntensity,ANY,missing,ANY.Rdash.method) 1061 0 R (Rfn.[,SolexaIntensity,missing,ANY,ANY.Rdash.method) 1062 0 R (Rfn.[,SolexaIntensity,missing,missing,ANY.Rdash.method) 1063 0 R (Rfn.[[,ArrayIntensity,ANY,ANY.Rdash.method) 472 0 R (Rfn.[[,MatrixQuality,ANY,missing.Rdash.method) 568 0 R (Rfn.[[,QualityScore,ANY,missing.Rdash.method) 569 0 R] /Limits [(Rfn.[,SolexaIntensity,ANY,missing,ANY.Rdash.method) (Rfn.[[,QualityScore,ANY,missing.Rdash.method)] >> endobj 2223 0 obj << /Names [(Rfn.[[,SRList,ANY,missing.Rdash.method) 855 0 R (Rfn.accessors) 325 0 R (Rfn.accessors.1) 126 0 R (Rfn.alignData) 1182 0 R (Rfn.alignDataFilter) 1566 0 R (Rfn.alignQuality) 1183 0 R] /Limits [(Rfn.[[,SRList,ANY,missing.Rdash.method) (Rfn.alignQuality)] >> endobj 2224 0 obj << /Names [(Rfn.alignQualityFilter) 1567 0 R (Rfn.alphabet,FastqQuality.Rdash.method) 530 0 R (Rfn.alphabetByCycle) 589 0 R (Rfn.alphabetByCycle,BStringSet.Rdash.method) 1209 0 R (Rfn.alphabetByCycle,FastqQuality.Rdash.method) 531 0 R (Rfn.alphabetByCycle,ShortRead.Rdash.method) 898 0 R] /Limits [(Rfn.alignQualityFilter) (Rfn.alphabetByCycle,ShortRead.Rdash.method)] >> endobj 2225 0 obj << /Names [(Rfn.alphabetByCycle,ShortReadQ.Rdash.method) 982 0 R (Rfn.alphabetByCycle.1) 130 0 R (Rfn.alphabetFrequency) 588 0 R (Rfn.alphabetFrequency,FastqQuality.Rdash.method) 532 0 R (Rfn.alphabetScore) 590 0 R (Rfn.alphabetScore,FastqQuality.Rdash.method) 533 0 R] /Limits [(Rfn.alphabetByCycle,ShortReadQ.Rdash.method) (Rfn.alphabetScore,FastqQuality.Rdash.method)] >> endobj 2226 0 obj << /Names [(Rfn.alphabetScore,SFastqQuality.Rdash.method) 534 0 R (Rfn.alphabetScore,ShortReadQ.Rdash.method) 983 0 R (Rfn.alphabetScore.1) 134 0 R (Rfn.analysisPath) 1184 0 R (Rfn.append,.ShortReadBase,.ShortReadBase,ANY.Rdash.method) 977 0 R (Rfn.append,AlignedDataFrame,AlignedDataFrame,missing.Rdash.method) 250 0 R] /Limits [(Rfn.alphabetScore,SFastqQuality.Rdash.method) (Rfn.append,AlignedDataFrame,AlignedDataFrame,missing.Rdash.method)] >> endobj 2227 0 obj << /Names [(Rfn.append,AlignedRead,AlignedRead,missing.Rdash.method) 278 0 R (Rfn.append,MatrixQuality,MatrixQuality,missing.Rdash.method) 535 0 R (Rfn.append,QualityScore,QualityScore,missing.Rdash.method) 536 0 R (Rfn.append,ShortRead,ShortRead,missing.Rdash.method) 899 0 R (Rfn.append,ShortReadQ,ShortReadQ,missing.Rdash.method) 984 0 R (Rfn.atomic) 803 0 R] /Limits [(Rfn.append,AlignedRead,AlignedRead,missing.Rdash.method) (Rfn.atomic)] >> endobj 2228 0 obj << /Names [(Rfn.baseCallPath) 1185 0 R (Rfn.basePath) 1266 0 R (Rfn.c,SRFilter.Rdash.method) 748 0 R (Rfn.chromosome) 1186 0 R (Rfn.chromosome,AlignedRead.Rdash.method) 279 0 R (Rfn.chromosomeFilter) 1568 0 R] /Limits [(Rfn.baseCallPath) (Rfn.chromosomeFilter)] >> endobj 2229 0 obj << /Names [(Rfn.clean) 1236 0 R (Rfn.clean,DNAStringSet.Rdash.method) 1237 0 R (Rfn.clean,ShortRead.Rdash.method) 900 0 R (Rfn.clean.1) 138 0 R (Rfn.coerce,AlignedRead,GRanges.Rdash.method) 281 0 R (Rfn.coerce,AlignedRead,GappedAlignments.Rdash.method) 280 0 R] /Limits [(Rfn.clean) (Rfn.coerce,AlignedRead,GappedAlignments.Rdash.method)] >> endobj 2230 0 obj << /Names [(Rfn.coerce,AlignedRead,RangedData.Rdash.method) 282 0 R (Rfn.coerce,AlignedRead,RangesList.Rdash.method) 283 0 R (Rfn.coerce,FastqQuality,PhredQuality.Rdash.method) 539 0 R (Rfn.coerce,FastqQuality,matrix.Rdash.method) 537 0 R (Rfn.coerce,FastqQuality,numeric.Rdash.method) 538 0 R (Rfn.coerce,PairwiseAlignedXStringSet,AlignedRead.Rdash.method) 284 0 R] /Limits [(Rfn.coerce,AlignedRead,RangedData.Rdash.method) (Rfn.coerce,PairwiseAlignedXStringSet,AlignedRead.Rdash.method)] >> endobj 2231 0 obj << /Names [(Rfn.coerce,SFastqQuality,SolexaQuality.Rdash.method) 541 0 R (Rfn.coerce,SFastqQuality,matrix.Rdash.method) 540 0 R (Rfn.coerce,SRFilter,FilterRules.Rdash.method) 749 0 R (Rfn.coerce,ShortReadQ,QualityScaledDNAStringSet.Rdash.method) 985 0 R (Rfn.compact,FastqQuality.Rdash.method) 542 0 R (Rfn.compact,ShortRead.Rdash.method) 901 0 R] /Limits [(Rfn.coerce,SFastqQuality,SolexaQuality.Rdash.method) (Rfn.compact,ShortRead.Rdash.method)] >> endobj 2232 0 obj << /Names [(Rfn.compact,ShortReadQ.Rdash.method) 986 0 R (Rfn.compose) 1569 0 R (Rfn.countLines) 1251 0 R (Rfn.countLines.1) 142 0 R (Rfn.coverage) 1425 0 R (Rfn.coverage,AlignedRead.Rdash.method) 285 0 R] /Limits [(Rfn.compact,ShortReadQ.Rdash.method) (Rfn.coverage,AlignedRead.Rdash.method)] >> endobj 2233 0 obj << /Names [(Rfn.dataPath) 1187 0 R (Rfn.deprecated) 1265 0 R (Rfn.deprecated.1) 146 0 R (Rfn.detail,.ShortReadBase.Rdash.method) 835 0 R (Rfn.detail,AlignedRead.Rdash.method) 286 0 R (Rfn.detail,ExperimentPath.Rdash.method) 411 0 R] /Limits [(Rfn.dataPath) (Rfn.detail,ExperimentPath.Rdash.method)] >> endobj 2234 0 obj << /Names [(Rfn.detail,QualityScore.Rdash.method) 543 0 R (Rfn.detail,RochePath.Rdash.method) 636 0 R (Rfn.detail,SRList.Rdash.method) 836 0 R (Rfn.detail,SRSet.Rdash.method) 812 0 R (Rfn.detail,SRVector.Rdash.method) 837 0 R (Rfn.detail,ShortRead.Rdash.method) 902 0 R] /Limits [(Rfn.detail,QualityScore.Rdash.method) (Rfn.detail,ShortRead.Rdash.method)] >> endobj 2235 0 obj << /Names [(Rfn.detail,ShortReadQ.Rdash.method) 987 0 R (Rfn.detail,SolexaPath.Rdash.method) 1109 0 R (Rfn.detail,SolexaSet.Rdash.method) 1154 0 R (Rfn.dim,Intensity.Rdash.method) 459 0 R (Rfn.dim,MatrixQuality.Rdash.method) 544 0 R (Rfn.dustyFilter) 1570 0 R] /Limits [(Rfn.detail,ShortReadQ.Rdash.method) (Rfn.dustyFilter)] >> endobj 2236 0 obj << /Names [(Rfn.dustyScore) 1280 0 R (Rfn.dustyScore,DNAStringSet.Rdash.method) 1281 0 R (Rfn.dustyScore,ShortRead.Rdash.method) 1282 0 R (Rfn.dustyScore.1) 150 0 R (Rfn.experimentPath) 1188 0 R (Rfn.experimentPath,SRSet.Rdash.method) 813 0 R] /Limits [(Rfn.dustyScore) (Rfn.experimentPath,SRSet.Rdash.method)] >> endobj 2237 0 obj << /Names [(Rfn.function.Rdash.class) 762 0 R (Rfn.grep) 1258 0 R (Rfn.id) 1189 0 R (Rfn.id,ShortRead.Rdash.method) 903 0 R (Rfn.idFilter) 1571 0 R (Rfn.imageAnalysisPath) 1190 0 R] /Limits [(Rfn.function.Rdash.class) (Rfn.imageAnalysisPath)] >> endobj 2238 0 obj << /Names [(Rfn.intensity) 460 0 R (Rfn.is) 860 0 R (Rfn.laneDescription) 1191 0 R (Rfn.laneNames) 1192 0 R (Rfn.laneNames,AnnotatedDataFrame.Rdash.method) 1155 0 R (Rfn.laneNames,SolexaSet.Rdash.method) 1156 0 R] /Limits [(Rfn.intensity) (Rfn.laneNames,SolexaSet.Rdash.method)] >> endobj 2239 0 obj << /Names [(Rfn.lapply) 870 0 R (Rfn.lapply,SRList,ANY.Rdash.method) 838 0 R (Rfn.lapply,SRList.Rdash.method) 839 0 R (Rfn.length,MatrixQuality.Rdash.method) 547 0 R (Rfn.length,QualityScore.Rdash.method) 548 0 R (Rfn.length,SRList.Rdash.method) 840 0 R] /Limits [(Rfn.lapply) (Rfn.length,SRList.Rdash.method)] >> endobj 2240 0 obj << /Names [(Rfn.length,ShortRead.Rdash.method) 904 0 R (Rfn.list.files) 1259 0 R (Rfn.logical.Rdash.class) 801 0 R (Rfn.measurementError) 463 0 R (Rfn.nFilter) 1572 0 R (Rfn.name) 750 0 R] /Limits [(Rfn.length,ShortRead.Rdash.method) (Rfn.name)] >> endobj 2241 0 obj << /Names [(Rfn.name,SRFilter.Rdash.method) 751 0 R (Rfn.name,SRFilterResult.Rdash.method) 776 0 R (Rfn.names,SRList.Rdash.method) 841 0 R (Rfn.names<.Rdash.,SRList,character.Rdash.method) 842 0 R (Rfn.narrow) 591 0 R (Rfn.narrow,FastqQuality.Rdash.method) 550 0 R] /Limits [(Rfn.name,SRFilter.Rdash.method) (Rfn.narrow,FastqQuality.Rdash.method)] >> endobj 2242 0 obj << /Names [(Rfn.narrow,MatrixQuality.Rdash.method) 551 0 R (Rfn.narrow,ShortRead.Rdash.method) 905 0 R (Rfn.narrow,ShortReadQ.Rdash.method) 988 0 R (Rfn.occurrenceFilter) 1573 0 R (Rfn.overlap) 339 0 R (Rfn.pairwiseAlignment) 1630 0 R] /Limits [(Rfn.narrow,MatrixQuality.Rdash.method) (Rfn.pairwiseAlignment)] >> endobj 2243 0 obj << /Names [(Rfn.phenoData,SRSet.Rdash.method) 814 0 R (Rfn.phenoData.Rdash.class) 825 0 R (Rfn.pileup) 1267 0 R (Rfn.polyn) 1301 0 R (Rfn.polynFilter) 1574 0 R (Rfn.position) 1193 0 R] /Limits [(Rfn.phenoData,SRSet.Rdash.method) (Rfn.position)] >> endobj 2244 0 obj << /Names [(Rfn.position,AlignedRead.Rdash.method) 287 0 R (Rfn.positionFilter) 1575 0 R (Rfn.qa) 377 0 R (Rfn.qa,ShortReadQ.Rdash.method) 989 0 R (Rfn.qa,SolexaPath.Rdash.method) 1110 0 R (Rfn.qa,character.Rdash.method) 1317 0 R] /Limits [(Rfn.position,AlignedRead.Rdash.method) (Rfn.qa,character.Rdash.method)] >> endobj 2245 0 obj << /Names [(Rfn.qa,list.Rdash.method) 1318 0 R (Rfn.qa.1) 158 0 R (Rfn.qualPath) 637 0 R (Rfn.rank) 1664 0 R (Rfn.rbind,.QA.Rdash.method) 514 0 R (Rfn.read454) 638 0 R] /Limits [(Rfn.qa,list.Rdash.method) (Rfn.read454)] >> endobj 2246 0 obj << /Names [(Rfn.read454,RochePath.Rdash.method) 639 0 R (Rfn.readAligned) 304 0 R (Rfn.readAligned,SolexaPath.Rdash.method) 1111 0 R (Rfn.readAligned,SolexaSet.Rdash.method) 1157 0 R (Rfn.readAligned,character.Rdash.method) 1340 0 R (Rfn.readAligned.1) 162 0 R] /Limits [(Rfn.read454,RochePath.Rdash.method) (Rfn.readAligned.1)] >> endobj 2247 0 obj << /Names [(Rfn.readBaseQuality) 1400 0 R (Rfn.readBaseQuality,RochePath.Rdash.method) 640 0 R (Rfn.readBaseQuality,SolexaPath.Rdash.method) 1112 0 R (Rfn.readBaseQuality,character.Rdash.method) 1401 0 R (Rfn.readBaseQuality.1) 166 0 R (Rfn.readBfaToc) 1273 0 R] /Limits [(Rfn.readBaseQuality) (Rfn.readBfaToc)] >> endobj 2248 0 obj << /Names [(Rfn.readBfaToc.1) 170 0 R (Rfn.readCount) 815 0 R (Rfn.readData) 816 0 R (Rfn.readFasta) 1420 0 R (Rfn.readFasta,RochePath.Rdash.method) 641 0 R (Rfn.readFasta,SolexaPath.Rdash.method) 1113 0 R] /Limits [(Rfn.readBfaToc.1) (Rfn.readFasta,SolexaPath.Rdash.method)] >> endobj 2249 0 obj << /Names [(Rfn.readFasta,character.Rdash.method) 1421 0 R (Rfn.readFasta.1) 174 0 R (Rfn.readFastaQual) 642 0 R (Rfn.readFastaQual,RochePath.Rdash.method) 644 0 R (Rfn.readFastaQual,character.Rdash.method) 643 0 R (Rfn.readFastq) 659 0 R] /Limits [(Rfn.readFasta,character.Rdash.method) (Rfn.readFastq)] >> endobj 2250 0 obj << /Names [(Rfn.readFastq,SolexaPath.Rdash.method) 1114 0 R (Rfn.readFastq,character.Rdash.method) 1437 0 R (Rfn.readFastq.1) 178 0 R (Rfn.readIndex) 817 0 R (Rfn.readInfo) 464 0 R (Rfn.readIntensities) 480 0 R] /Limits [(Rfn.readFastq,SolexaPath.Rdash.method) (Rfn.readIntensities)] >> endobj 2251 0 obj << /Names [(Rfn.readIntensities,SolexaPath.Rdash.method) 1115 0 R (Rfn.readIntensities,character.Rdash.method) 1141 0 R (Rfn.readIntensities.1) 182 0 R (Rfn.readPath) 645 0 R (Rfn.readPrb) 1409 0 R (Rfn.readPrb,SolexaPath.Rdash.method) 1116 0 R] /Limits [(Rfn.readIntensities,SolexaPath.Rdash.method) (Rfn.readPrb,SolexaPath.Rdash.method)] >> endobj 2252 0 obj << /Names [(Rfn.readPrb,character.Rdash.method) 1142 0 R (Rfn.readPrb.1) 186 0 R (Rfn.readQseq) 1496 0 R (Rfn.readQseq,SolexaPath.Rdash.method) 1117 0 R (Rfn.readQseq,character.Rdash.method) 1143 0 R (Rfn.readQseq.1) 190 0 R] /Limits [(Rfn.readPrb,character.Rdash.method) (Rfn.readQseq.1)] >> endobj 2253 0 obj << /Names [(Rfn.readQual) 646 0 R (Rfn.readQual,RochePath.Rdash.method) 648 0 R (Rfn.readQual,character.Rdash.method) 647 0 R (Rfn.readXStringColumns) 1362 0 R (Rfn.readXStringColumns.1) 194 0 R (Rfn.renew) 1520 0 R] /Limits [(Rfn.readQual) (Rfn.renew)] >> endobj 2254 0 obj << /Names [(Rfn.renew,.ShortReadBase.Rdash.method) 1521 0 R (Rfn.renewable) 1519 0 R (Rfn.renewable,.ShortReadBase.Rdash.method) 1522 0 R (Rfn.renewable,character.Rdash.method) 1523 0 R (Rfn.renewable,missing.Rdash.method) 1524 0 R (Rfn.renewable.1) 198 0 R] /Limits [(Rfn.renew,.ShortReadBase.Rdash.method) (Rfn.renewable.1)] >> endobj 2255 0 obj << /Names [(Rfn.report) 1323 0 R (Rfn.report,ANY.Rdash.method) 1546 0 R (Rfn.report,BAMQA.Rdash.method) 367 0 R (Rfn.report,BowtieQA.Rdash.method) 393 0 R (Rfn.report,FastqQA.Rdash.method) 437 0 R (Rfn.report,MAQMapQA.Rdash.method) 498 0 R] /Limits [(Rfn.report) (Rfn.report,MAQMapQA.Rdash.method)] >> endobj 2256 0 obj << /Names [(Rfn.report,SolexaExportQA.Rdash.method) 1037 0 R (Rfn.report,SolexaPath.Rdash.method) 1118 0 R (Rfn.report.1) 202 0 R (Rfn.report.Rul.html) 1547 0 R (Rfn.report.Rul.html,BAMQA.Rdash.method) 368 0 R (Rfn.report.Rul.html,BowtieQA.Rdash.method) 394 0 R] /Limits [(Rfn.report,SolexaExportQA.Rdash.method) (Rfn.report.Rul.html,BowtieQA.Rdash.method)] >> endobj 2257 0 obj << /Names [(Rfn.report.Rul.html,FastqQA.Rdash.method) 438 0 R (Rfn.report.Rul.html,MAQMapQA.Rdash.method) 499 0 R (Rfn.report.Rul.html,ShortReadQQA.Rdash.method) 439 0 R (Rfn.report.Rul.html,SolexaExportQA.Rdash.method) 1038 0 R (Rfn.report.Rul.html,SolexaRealignQA.Rdash.method) 1039 0 R (Rfn.runNames) 652 0 R] /Limits [(Rfn.report.Rul.html,FastqQA.Rdash.method) (Rfn.runNames)] >> endobj 2258 0 obj << /Names [(Rfn.runNames,RochePath.Rdash.method) 653 0 R (Rfn.sapply) 871 0 R (Rfn.sapply,SRList.Rdash.method) 843 0 R (Rfn.scanPath) 1194 0 R (Rfn.show,.QA.Rdash.method) 515 0 R (Rfn.show,.ShortReadBase.Rdash.method) 978 0 R] /Limits [(Rfn.runNames,RochePath.Rdash.method) (Rfn.show,.ShortReadBase.Rdash.method)] >> endobj 2259 0 obj << /Names [(Rfn.show,AlignedRead.Rdash.method) 288 0 R (Rfn.show,ExperimentPath.Rdash.method) 413 0 R (Rfn.show,FastqQuality.Rdash.method) 554 0 R (Rfn.show,FastqSampler.Rdash.method) 881 0 R (Rfn.show,Intensity.Rdash.method) 465 0 R (Rfn.show,IntensityMeasure.Rdash.method) 466 0 R] /Limits [(Rfn.show,AlignedRead.Rdash.method) (Rfn.show,IntensityMeasure.Rdash.method)] >> endobj 2260 0 obj << /Names [(Rfn.show,NumericQuality.Rdash.method) 555 0 R (Rfn.show,RochePath.Rdash.method) 654 0 R (Rfn.show,SRFilter.Rdash.method) 752 0 R (Rfn.show,SRFilterResult.Rdash.method) 777 0 R (Rfn.show,SRList.Rdash.method) 844 0 R (Rfn.show,SRSet.Rdash.method) 818 0 R] /Limits [(Rfn.show,NumericQuality.Rdash.method) (Rfn.show,SRSet.Rdash.method)] >> endobj 2261 0 obj << /Names [(Rfn.show,SRVector.Rdash.method) 845 0 R (Rfn.show,ShortRead.Rdash.method) 910 0 R (Rfn.show,SolexaExportQA.Rdash.method) 1040 0 R (Rfn.show,SolexaPath.Rdash.method) 1119 0 R (Rfn.show,SolexaSet.Rdash.method) 1158 0 R (Rfn.solexaPath) 1195 0 R] /Limits [(Rfn.show,SRVector.Rdash.method) (Rfn.solexaPath)] >> endobj 2262 0 obj << /Names [(Rfn.sourcePath) 819 0 R (Rfn.sprintf) 859 0 R (Rfn.srFilter) 761 0 R (Rfn.srFilter,SRFilter.Rdash.method) 753 0 R (Rfn.srFilter,function.Rdash.method) 1577 0 R (Rfn.srFilter,missing.Rdash.method) 1578 0 R] /Limits [(Rfn.sourcePath) (Rfn.srFilter,missing.Rdash.method)] >> endobj 2263 0 obj << /Names [(Rfn.srFilter.1) 206 0 R (Rfn.srapply) 1343 0 R (Rfn.srapply.1) 210 0 R (Rfn.srdistance) 944 0 R (Rfn.srdistance,DNAStringSet,DNAString.Rdash.method) 1625 0 R (Rfn.srdistance,DNAStringSet,DNAStringSet.Rdash.method) 1626 0 R] /Limits [(Rfn.srFilter.1) (Rfn.srdistance,DNAStringSet,DNAStringSet.Rdash.method)] >> endobj 2264 0 obj << /Names [(Rfn.srdistance,DNAStringSet,character.Rdash.method) 1624 0 R (Rfn.srdistance,ShortRead,ANY.Rdash.method) 911 0 R (Rfn.srdistance.1) 214 0 R (Rfn.srdistanceFilter) 1576 0 R (Rfn.srduplicated) 1642 0 R (Rfn.srduplicated,AlignedRead.Rdash.method) 289 0 R] /Limits [(Rfn.srdistance,DNAStringSet,character.Rdash.method) (Rfn.srduplicated,AlignedRead.Rdash.method)] >> endobj 2265 0 obj << /Names [(Rfn.srduplicated,FastqQuality.Rdash.method) 556 0 R (Rfn.srduplicated,ShortRead.Rdash.method) 912 0 R (Rfn.srduplicated,XStringSet.Rdash.method) 1643 0 R (Rfn.srduplicated.1) 218 0 R (Rfn.sread) 1196 0 R (Rfn.srorder) 1644 0 R] /Limits [(Rfn.srduplicated,FastqQuality.Rdash.method) (Rfn.srorder)] >> endobj 2266 0 obj << /Names [(Rfn.srorder,AlignedRead.Rdash.method) 290 0 R (Rfn.srorder,FastqQuality.Rdash.method) 557 0 R (Rfn.srorder,ShortRead.Rdash.method) 913 0 R (Rfn.srorder,XStringSet.Rdash.method) 1645 0 R (Rfn.srrank) 1646 0 R (Rfn.srrank,AlignedRead.Rdash.method) 291 0 R] /Limits [(Rfn.srorder,AlignedRead.Rdash.method) (Rfn.srrank,AlignedRead.Rdash.method)] >> endobj 2267 0 obj << /Names [(Rfn.srrank,FastqQuality.Rdash.method) 558 0 R (Rfn.srrank,ShortRead.Rdash.method) 914 0 R (Rfn.srrank,XStringSet.Rdash.method) 1647 0 R (Rfn.srsort) 621 0 R (Rfn.srsort,FastqQuality.Rdash.method) 559 0 R (Rfn.srsort,ShortRead.Rdash.method) 915 0 R] /Limits [(Rfn.srrank,FastqQuality.Rdash.method) (Rfn.srsort,ShortRead.Rdash.method)] >> endobj 2268 0 obj << /Names [(Rfn.srsort,XStringSet.Rdash.method) 1648 0 R (Rfn.stats) 779 0 R (Rfn.stats,SRFilterResult.Rdash.method) 780 0 R (Rfn.strand,AlignedRead.Rdash.method) 292 0 R (Rfn.strandFilter) 1579 0 R (Rfn.tables) 963 0 R] /Limits [(Rfn.srsort,XStringSet.Rdash.method) (Rfn.tables)] >> endobj 2269 0 obj << /Names [(Rfn.tables,ShortRead.Rdash.method) 916 0 R (Rfn.tables,XStringSet.Rdash.method) 1671 0 R (Rfn.tables.1) 222 0 R (Rfn.tapply) 1607 0 R (Rfn.trimLRPatterns) 945 0 R (Rfn.trimLRPatterns,ShortRead.Rdash.method) 917 0 R] /Limits [(Rfn.tables,ShortRead.Rdash.method) (Rfn.trimLRPatterns,ShortRead.Rdash.method)] >> endobj 2270 0 obj << /Names [(Rfn.uniqueFilter) 959 0 R (Rfn.vclass) 1197 0 R (Rfn.vector.Rdash.class) 802 0 R (Rfn.width,FastqQuality.Rdash.method) 560 0 R (Rfn.width,MatrixQuality.Rdash.method) 561 0 R (Rfn.width,NumericQuality.Rdash.method) 562 0 R] /Limits [(Rfn.uniqueFilter) (Rfn.width,NumericQuality.Rdash.method)] >> endobj 2271 0 obj << /Names [(Rfn.width,QualityScore.Rdash.method) 563 0 R (Rfn.width,ShortRead.Rdash.method) 918 0 R (Rfn.writeFASTA) 964 0 R (Rfn.writeFasta) 1422 0 R (Rfn.writeFasta,ShortRead.Rdash.method) 919 0 R (Rfn.writeFastq) 1438 0 R] /Limits [(Rfn.width,QualityScore.Rdash.method) (Rfn.writeFastq)] >> endobj 2272 0 obj << /Names [(Rfn.writeFastq,ShortReadQ.Rdash.method) 995 0 R (Rfn.yield) 882 0 R (Rfn.yield,FastqSampler.Rdash.method) 883 0 R (chapter*.1) 244 0 R (index.0) 226 0 R (page.1) 242 0 R] /Limits [(Rfn.writeFastq,ShortReadQ.Rdash.method) (page.1)] >> endobj 2273 0 obj << /Names [(page.10) 455 0 R (page.11) 492 0 R (page.12) 510 0 R (page.13) 528 0 R (page.14) 586 0 R (page.15) 603 0 R] /Limits [(page.10) (page.15)] >> endobj 2274 0 obj << /Names [(page.16) 631 0 R (page.17) 668 0 R (page.18) 686 0 R (page.19) 708 0 R (page.2) 268 0 R (page.20) 725 0 R] /Limits [(page.16) (page.20)] >> endobj 2275 0 obj << /Names [(page.21) 746 0 R (page.22) 771 0 R (page.23) 794 0 R (page.24) 811 0 R (page.25) 831 0 R (page.26) 866 0 R] /Limits [(page.21) (page.26)] >> endobj 2276 0 obj << /Names [(page.27) 876 0 R (page.28) 894 0 R (page.29) 941 0 R (page.3) 318 0 R (page.30) 954 0 R (page.31) 973 0 R] /Limits [(page.27) (page.31)] >> endobj 2277 0 obj << /Names [(page.32) 1020 0 R (page.33) 1032 0 R (page.34) 1053 0 R (page.35) 1084 0 R (page.36) 1095 0 R (page.37) 1108 0 R] /Limits [(page.32) (page.37)] >> endobj 2278 0 obj << /Names [(page.38) 1138 0 R (page.39) 1150 0 R (page.4) 335 0 R (page.40) 1170 0 R (page.41) 1180 0 R (page.42) 1204 0 R] /Limits [(page.38) (page.42)] >> endobj 2279 0 obj << /Names [(page.43) 1221 0 R (page.44) 1234 0 R (page.45) 1250 0 R (page.46) 1264 0 R (page.47) 1277 0 R (page.48) 1291 0 R] /Limits [(page.43) (page.48)] >> endobj 2280 0 obj << /Names [(page.49) 1311 0 R (page.5) 347 0 R (page.50) 1334 0 R (page.51) 1350 0 R (page.52) 1361 0 R (page.53) 1367 0 R] /Limits [(page.49) (page.53)] >> endobj 2281 0 obj << /Names [(page.54) 1373 0 R (page.55) 1384 0 R (page.56) 1399 0 R (page.57) 1414 0 R (page.58) 1432 0 R (page.59) 1447 0 R] /Limits [(page.54) (page.59)] >> endobj 2282 0 obj << /Names [(page.6) 365 0 R (page.60) 1457 0 R (page.61) 1467 0 R (page.62) 1478 0 R (page.63) 1491 0 R (page.64) 1504 0 R] /Limits [(page.6) (page.64)] >> endobj 2283 0 obj << /Names [(page.65) 1515 0 R (page.66) 1529 0 R (page.67) 1545 0 R (page.68) 1561 0 R (page.69) 1586 0 R (page.7) 391 0 R] /Limits [(page.65) (page.7)] >> endobj 2284 0 obj << /Names [(page.70) 1594 0 R (page.71) 1602 0 R (page.72) 1611 0 R (page.73) 1619 0 R (page.74) 1635 0 R (page.75) 1658 0 R] /Limits [(page.70) (page.75)] >> endobj 2285 0 obj << /Names [(page.76) 1669 0 R (page.77) 1680 0 R (page.78) 1752 0 R (page.79) 1815 0 R (page.8) 409 0 R (page.80) 1874 0 R] /Limits [(page.76) (page.80)] >> endobj 2286 0 obj << /Names [(page.81) 1929 0 R (page.82) 1990 0 R (page.83) 2053 0 R (page.84) 2115 0 R (page.85) 2163 0 R (page.9) 433 0 R] /Limits [(page.81) (page.9)] >> endobj 2287 0 obj << /Names [(section*.10) 273 0 R (section*.100) 669 0 R (section*.101) 670 0 R (section*.102) 671 0 R (section*.103) 672 0 R (section*.104) 688 0 R] /Limits [(section*.10) (section*.104)] >> endobj 2288 0 obj << /Names [(section*.105) 689 0 R (section*.106) 690 0 R (section*.107) 691 0 R (section*.108) 692 0 R (section*.109) 693 0 R (section*.11) 274 0 R] /Limits [(section*.105) (section*.11)] >> endobj 2289 0 obj << /Names [(section*.110) 694 0 R (section*.111) 695 0 R (section*.112) 710 0 R (section*.113) 711 0 R (section*.114) 712 0 R (section*.115) 713 0 R] /Limits [(section*.110) (section*.115)] >> endobj 2290 0 obj << /Names [(section*.116) 714 0 R (section*.117) 715 0 R (section*.118) 716 0 R (section*.119) 717 0 R (section*.12) 275 0 R (section*.120) 727 0 R] /Limits [(section*.116) (section*.120)] >> endobj 2291 0 obj << /Names [(section*.121) 728 0 R (section*.122) 729 0 R (section*.123) 730 0 R (section*.124) 731 0 R (section*.125) 732 0 R (section*.126) 733 0 R] /Limits [(section*.121) (section*.126)] >> endobj 2292 0 obj << /Names [(section*.127) 754 0 R (section*.128) 755 0 R (section*.129) 756 0 R (section*.13) 276 0 R (section*.130) 757 0 R (section*.131) 758 0 R] /Limits [(section*.127) (section*.131)] >> endobj 2293 0 obj << /Names [(section*.132) 759 0 R (section*.133) 760 0 R (section*.134) 772 0 R (section*.135) 781 0 R (section*.136) 782 0 R (section*.137) 783 0 R] /Limits [(section*.132) (section*.137)] >> endobj 2294 0 obj << /Names [(section*.138) 784 0 R (section*.139) 795 0 R (section*.14) 301 0 R (section*.140) 796 0 R (section*.141) 797 0 R (section*.142) 798 0 R] /Limits [(section*.138) (section*.142)] >> endobj 2295 0 obj << /Names [(section*.143) 799 0 R (section*.144) 800 0 R (section*.145) 820 0 R (section*.146) 821 0 R (section*.147) 822 0 R (section*.148) 823 0 R] /Limits [(section*.143) (section*.148)] >> endobj 2296 0 obj << /Names [(section*.149) 824 0 R (section*.15) 302 0 R (section*.150) 832 0 R (section*.151) 833 0 R (section*.152) 856 0 R (section*.153) 857 0 R] /Limits [(section*.149) (section*.153)] >> endobj 2297 0 obj << /Names [(section*.154) 867 0 R (section*.155) 868 0 R (section*.156) 869 0 R (section*.157) 877 0 R (section*.158) 884 0 R (section*.159) 885 0 R] /Limits [(section*.154) (section*.159)] >> endobj 2298 0 obj << /Names [(section*.16) 319 0 R (section*.160) 886 0 R (section*.161) 887 0 R (section*.162) 895 0 R (section*.163) 896 0 R (section*.164) 897 0 R] /Limits [(section*.16) (section*.164)] >> endobj 2299 0 obj << /Names [(section*.165) 928 0 R (section*.166) 929 0 R (section*.167) 930 0 R (section*.168) 942 0 R (section*.169) 943 0 R (section*.17) 320 0 R] /Limits [(section*.165) (section*.17)] >> endobj 2300 0 obj << /Names [(section*.170) 955 0 R (section*.171) 956 0 R (section*.172) 957 0 R (section*.173) 960 0 R (section*.174) 961 0 R (section*.175) 962 0 R] /Limits [(section*.170) (section*.175)] >> endobj 2301 0 obj << /Names [(section*.176) 974 0 R (section*.177) 979 0 R (section*.178) 980 0 R (section*.179) 981 0 R (section*.18) 321 0 R (section*.180) 1004 0 R] /Limits [(section*.176) (section*.180)] >> endobj 2302 0 obj << /Names [(section*.181) 1005 0 R (section*.182) 1006 0 R (section*.183) 1007 0 R (section*.184) 1021 0 R (section*.185) 1033 0 R (section*.186) 1034 0 R] /Limits [(section*.181) (section*.186)] >> endobj 2303 0 obj << /Names [(section*.187) 1035 0 R (section*.188) 1043 0 R (section*.189) 1044 0 R (section*.19) 336 0 R (section*.190) 1045 0 R (section*.191) 1046 0 R] /Limits [(section*.187) (section*.191)] >> endobj 2304 0 obj << /Names [(section*.192) 1054 0 R (section*.193) 1055 0 R (section*.194) 1056 0 R (section*.195) 1057 0 R (section*.196) 1064 0 R (section*.197) 1065 0 R] /Limits [(section*.192) (section*.197)] >> endobj 2305 0 obj << /Names [(section*.198) 1066 0 R (section*.199) 1085 0 R (section*.2) 251 0 R (section*.20) 337 0 R (section*.200) 1086 0 R (section*.201) 1087 0 R] /Limits [(section*.198) (section*.201)] >> endobj 2306 0 obj << /Names [(section*.202) 1088 0 R (section*.203) 1089 0 R (section*.204) 1097 0 R (section*.205) 1098 0 R (section*.206) 1099 0 R (section*.207) 1100 0 R] /Limits [(section*.202) (section*.207)] >> endobj 2307 0 obj << /Names [(section*.208) 1101 0 R (section*.209) 1102 0 R (section*.21) 338 0 R (section*.210) 1122 0 R (section*.211) 1123 0 R (section*.212) 1124 0 R] /Limits [(section*.208) (section*.212)] >> endobj 2308 0 obj << /Names [(section*.213) 1125 0 R (section*.214) 1139 0 R (section*.215) 1151 0 R (section*.216) 1152 0 R (section*.217) 1161 0 R (section*.218) 1171 0 R] /Limits [(section*.213) (section*.218)] >> endobj 2309 0 obj << /Names [(section*.219) 1172 0 R (section*.22) 348 0 R (section*.220) 1173 0 R (section*.221) 1174 0 R (section*.222) 1175 0 R (section*.223) 1181 0 R] /Limits [(section*.219) (section*.223)] >> endobj 2310 0 obj << /Names [(section*.224) 1198 0 R (section*.225) 1199 0 R (section*.226) 1205 0 R (section*.227) 1206 0 R (section*.228) 1207 0 R (section*.229) 1208 0 R] /Limits [(section*.224) (section*.229)] >> endobj 2311 0 obj << /Names [(section*.23) 349 0 R (section*.230) 1210 0 R (section*.231) 1211 0 R (section*.232) 1212 0 R (section*.233) 1213 0 R (section*.234) 1222 0 R] /Limits [(section*.23) (section*.234)] >> endobj 2312 0 obj << /Names [(section*.235) 1223 0 R (section*.236) 1224 0 R (section*.237) 1225 0 R (section*.238) 1226 0 R (section*.239) 1227 0 R (section*.24) 350 0 R] /Limits [(section*.235) (section*.24)] >> endobj 2313 0 obj << /Names [(section*.240) 1228 0 R (section*.241) 1229 0 R (section*.242) 1235 0 R (section*.243) 1238 0 R (section*.244) 1239 0 R (section*.245) 1240 0 R] /Limits [(section*.240) (section*.245)] >> endobj 2314 0 obj << /Names [(section*.246) 1241 0 R (section*.247) 1242 0 R (section*.248) 1243 0 R (section*.249) 1244 0 R (section*.25) 351 0 R (section*.250) 1252 0 R] /Limits [(section*.246) (section*.250)] >> endobj 2315 0 obj << /Names [(section*.251) 1253 0 R (section*.252) 1254 0 R (section*.253) 1255 0 R (section*.254) 1256 0 R (section*.255) 1257 0 R (section*.256) 1268 0 R] /Limits [(section*.251) (section*.256)] >> endobj 2316 0 obj << /Names [(section*.257) 1269 0 R (section*.258) 1270 0 R (section*.259) 1271 0 R (section*.26) 352 0 R (section*.260) 1272 0 R (section*.261) 1278 0 R] /Limits [(section*.257) 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1341 0 R (section*.288) 1342 0 R (section*.289) 1351 0 R] /Limits [(section*.284) (section*.289)] >> endobj 2322 0 obj << /Names [(section*.29) 370 0 R (section*.290) 1352 0 R (section*.291) 1385 0 R (section*.292) 1386 0 R (section*.293) 1387 0 R (section*.294) 1388 0 R] /Limits [(section*.29) (section*.294)] >> endobj 2323 0 obj << /Names [(section*.295) 1402 0 R (section*.296) 1403 0 R (section*.297) 1404 0 R (section*.298) 1405 0 R (section*.299) 1406 0 R (section*.3) 252 0 R] /Limits [(section*.295) (section*.3)] >> endobj 2324 0 obj << /Names [(section*.30) 371 0 R (section*.300) 1407 0 R (section*.301) 1408 0 R (section*.302) 1415 0 R (section*.303) 1416 0 R (section*.304) 1417 0 R] /Limits [(section*.30) (section*.304)] >> endobj 2325 0 obj << /Names [(section*.305) 1418 0 R (section*.306) 1419 0 R (section*.307) 1423 0 R (section*.308) 1424 0 R (section*.309) 1433 0 R (section*.31) 372 0 R] /Limits [(section*.305) (section*.31)] >> endobj 2326 0 obj << /Names [(section*.310) 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1565 0 R (section*.362) 1580 0 R (section*.363) 1587 0 R (section*.364) 1588 0 R] /Limits [(section*.36) (section*.364)] >> endobj 2336 0 obj << /Names [(section*.365) 1595 0 R (section*.366) 1603 0 R (section*.367) 1604 0 R (section*.368) 1605 0 R (section*.369) 1606 0 R (section*.37) 396 0 R] /Limits [(section*.365) (section*.37)] >> endobj 2337 0 obj << /Names [(section*.370) 1612 0 R (section*.371) 1613 0 R (section*.372) 1614 0 R (section*.373) 1620 0 R (section*.374) 1621 0 R (section*.375) 1622 0 R] /Limits [(section*.370) (section*.375)] >> endobj 2338 0 obj << /Names [(section*.376) 1623 0 R (section*.377) 1627 0 R (section*.378) 1628 0 R (section*.379) 1636 0 R (section*.38) 397 0 R (section*.380) 1637 0 R] /Limits [(section*.376) (section*.380)] >> endobj 2339 0 obj << /Names [(section*.381) 1638 0 R (section*.382) 1639 0 R (section*.383) 1640 0 R (section*.384) 1641 0 R (section*.385) 1649 0 R (section*.386) 1659 0 R] /Limits [(section*.381) (section*.386)] >> endobj 2340 0 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