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/Prev 7 0 R /Next 15 0 R >> endobj 7 0 obj << /Title 8 0 R /A 5 0 R /Parent 1927 0 R /Next 11 0 R >> endobj 1928 0 obj << /Names [(Doc-Start) 252 0 R (Rfn..QA.Rdash.class) 489 0 R (Rfn..QA.Rdash.class.1) 82 0 R (Rfn..Roche.Rdash.class) 1023 0 R (Rfn..SRUtil.Rdash.class) 490 0 R (Rfn..ShortReadBase.Rdash.class) 424 0 R] /Limits [(Doc-Start) (Rfn..ShortReadBase.Rdash.class)] >> endobj 1929 0 obj << /Names [(Rfn..Solexa.Rdash.class) 1101 0 R (Rfn.AlignedDataFrame) 372 0 R (Rfn.AlignedDataFrame.1) 14 0 R (Rfn.AlignedDataFrame.Rdash.class) 363 0 R (Rfn.AlignedDataFrame.Rdash.class.1) 10 0 R (Rfn.AlignedRead) 421 0 R] /Limits [(Rfn..Solexa.Rdash.class) (Rfn.AlignedRead)] >> endobj 1930 0 obj << /Names [(Rfn.AlignedRead.1) 22 0 R (Rfn.AlignedRead.Rdash.class) 371 0 R (Rfn.AlignedRead.Rdash.class.1) 18 0 R (Rfn.AnnotatedDataFrame) 370 0 R (Rfn.ArrayIntensity) 608 0 R (Rfn.ArrayIntensity.Rdash.class) 609 0 R] /Limits [(Rfn.AlignedRead.1) (Rfn.ArrayIntensity.Rdash.class)] >> endobj 1931 0 obj << /Names [(Rfn.BStringSet) 812 0 R (Rfn.BowtieQA.Rdash.class) 480 0 R (Rfn.BowtieQA.Rdash.class.1) 34 0 R (Rfn.ExperimentPath) 569 0 R (Rfn.ExperimentPath.Rdash.class) 567 0 R (Rfn.ExperimentPath.Rdash.class.1) 58 0 R] /Limits [(Rfn.BStringSet) (Rfn.ExperimentPath.Rdash.class.1)] >> endobj 1932 0 obj << /Names [(Rfn.FastqQA) 590 0 R (Rfn.FastqQA.Rdash.class) 589 0 R (Rfn.FastqQA.Rdash.class.1) 62 0 R (Rfn.FastqQuality) 767 0 R (Rfn.FastqQuality,BStringSet.Rdash.method) 796 0 R (Rfn.FastqQuality,character.Rdash.method) 797 0 R] /Limits [(Rfn.FastqQA) (Rfn.FastqQuality,character.Rdash.method)] >> endobj 1933 0 obj << /Names [(Rfn.FastqQuality,missing.Rdash.method) 798 0 R (Rfn.FastqQuality.Rdash.class) 737 0 R (Rfn.IntegerQuality) 799 0 R (Rfn.IntegerQuality.Rdash.class) 738 0 R (Rfn.Intensity.Rdash.class) 607 0 R (Rfn.Intensity.Rdash.class.1) 66 0 R] /Limits [(Rfn.FastqQuality,missing.Rdash.method) (Rfn.Intensity.Rdash.class.1)] >> endobj 1934 0 obj << /Names [(Rfn.IntensityInfo.Rdash.class) 612 0 R (Rfn.IntensityMeasure.Rdash.class) 613 0 R (Rfn.MAQMapQA) 647 0 R (Rfn.MAQMapQA.Rdash.class) 646 0 R (Rfn.MAQMapQA.Rdash.class.1) 70 0 R (Rfn.MatrixQuality) 800 0 R] /Limits [(Rfn.IntensityInfo.Rdash.class) (Rfn.MatrixQuality)] >> endobj 1935 0 obj << /Names [(Rfn.MatrixQuality.Rdash.class) 741 0 R (Rfn.NumericQuality) 766 0 R (Rfn.NumericQuality.Rdash.class) 744 0 R (Rfn.OptionalFunction.Rdash.class) 1380 0 R (Rfn.PossibleMethod.Rdash.class) 1381 0 R (Rfn.QualityScore) 795 0 R] /Limits [(Rfn.MatrixQuality.Rdash.class) (Rfn.QualityScore)] >> endobj 1936 0 obj << /Names [(Rfn.QualityScore.1) 94 0 R (Rfn.QualityScore.Rdash.class) 486 0 R (Rfn.QualityScore.Rdash.class.1) 90 0 R (Rfn.RochePath) 999 0 R (Rfn.RochePath.Rdash.class) 987 0 R (Rfn.RochePath.Rdash.class.1) 134 0 R] /Limits [(Rfn.QualityScore.1) (Rfn.RochePath.Rdash.class.1)] >> endobj 1937 0 obj << /Names [(Rfn.RocheSet) 1038 0 R (Rfn.RocheSet,RochePath.Rdash.method) 1001 0 R (Rfn.RocheSet,character.Rdash.method) 1000 0 R (Rfn.RocheSet.Rdash.class) 1024 0 R (Rfn.RocheSet.Rdash.class.1) 138 0 R (Rfn.SFastqQuality) 801 0 R] /Limits [(Rfn.RocheSet) (Rfn.SFastqQuality)] >> endobj 1938 0 obj << /Names [(Rfn.SFastqQuality,BStringSet.Rdash.method) 802 0 R (Rfn.SFastqQuality,character.Rdash.method) 803 0 R (Rfn.SFastqQuality,missing.Rdash.method) 804 0 R (Rfn.SFastqQuality.Rdash.class) 745 0 R (Rfn.SRError) 1447 0 R (Rfn.SRError.Rdash.class) 1448 0 R] /Limits [(Rfn.SFastqQuality,BStringSet.Rdash.method) (Rfn.SRError.Rdash.class)] >> endobj 1939 0 obj << /Names [(Rfn.SRFilter.Rdash.class) 826 0 R (Rfn.SRFilter.Rdash.class.1) 186 0 R (Rfn.SRList) 1449 0 R (Rfn.SRList.Rdash.class) 488 0 R (Rfn.SRSet.Rdash.class) 1047 0 R (Rfn.SRSet.Rdash.class.1) 194 0 R] /Limits [(Rfn.SRFilter.Rdash.class) (Rfn.SRSet.Rdash.class.1)] >> endobj 1940 0 obj << /Names [(Rfn.SRUtil.Rdash.class) 1435 0 R (Rfn.SRUtil.Rdash.class.1) 198 0 R (Rfn.SRVector) 1450 0 R (Rfn.SRVector.Rdash.class) 1451 0 R (Rfn.SRWarn) 1452 0 R (Rfn.SRWarn.Rdash.class) 1453 0 R] /Limits [(Rfn.SRUtil.Rdash.class) (Rfn.SRWarn.Rdash.class)] >> endobj 1941 0 obj << /Names [(Rfn.ShortRead) 1060 0 R (Rfn.ShortRead,DNAStringSet,BStringSet.Rdash.method) 1061 0 R (Rfn.ShortRead,DNAStringSet,missing.Rdash.method) 1062 0 R (Rfn.ShortRead,missing,missing.Rdash.method) 1063 0 R (Rfn.ShortRead.Rdash.class) 423 0 R (Rfn.ShortRead.Rdash.class.1) 142 0 R] /Limits [(Rfn.ShortRead) (Rfn.ShortRead.Rdash.class.1)] >> endobj 1942 0 obj << /Names [(Rfn.ShortReadBase.Rdash.package) 1100 0 R (Rfn.ShortReadBase.Rdash.package.1) 146 0 R (Rfn.ShortReadQ) 1107 0 R (Rfn.ShortReadQ,DNAStringSet,QualityScore,BStringSet.Rdash.method) 1126 0 R (Rfn.ShortReadQ,DNAStringSet,QualityScore,missing.Rdash.method) 1127 0 R (Rfn.ShortReadQ,missing,missing,missing.Rdash.method) 1128 0 R] /Limits [(Rfn.ShortReadBase.Rdash.package) (Rfn.ShortReadQ,missing,missing,missing.Rdash.method)] >> endobj 1943 0 obj << /Names [(Rfn.ShortReadQ.Rdash.class) 369 0 R (Rfn.ShortReadQ.Rdash.class.1) 150 0 R (Rfn.SolexaExportQA) 1162 0 R (Rfn.SolexaExportQA.Rdash.class) 697 0 R (Rfn.SolexaExportQA.Rdash.class.1) 154 0 R (Rfn.SolexaIntensity) 630 0 R] /Limits [(Rfn.ShortReadQ.Rdash.class) (Rfn.SolexaIntensity)] >> endobj 1944 0 obj << /Names [(Rfn.SolexaIntensity.1) 162 0 R (Rfn.SolexaIntensity.Rdash.class) 629 0 R (Rfn.SolexaIntensity.Rdash.class.1) 158 0 R (Rfn.SolexaIntensityInfo) 1214 0 R (Rfn.SolexaIntensityInfo.Rdash.class) 1178 0 R (Rfn.SolexaPath) 718 0 R] /Limits [(Rfn.SolexaIntensity.1) (Rfn.SolexaPath)] >> endobj 1945 0 obj << /Names [(Rfn.SolexaPath.Rdash.class) 576 0 R (Rfn.SolexaPath.Rdash.class.1) 166 0 R (Rfn.SolexaSet) 1269 0 R (Rfn.SolexaSet,SolexaPath.Rdash.method) 1237 0 R (Rfn.SolexaSet,character.Rdash.method) 1270 0 R (Rfn.SolexaSet.Rdash.class) 837 0 R] /Limits [(Rfn.SolexaPath.Rdash.class) (Rfn.SolexaSet.Rdash.class)] >> endobj 1946 0 obj << /Names [(Rfn.SolexaSet.Rdash.class.1) 170 0 R (Rfn.Utilites) 674 0 R (Rfn.Utilites.1) 78 0 R (Rfn.Versioned) 387 0 R (Rfn.XStringSet) 463 0 R (Rfn.[,AlignedRead,ANY,ANY,ANY.Rdash.method) 408 0 R] /Limits [(Rfn.SolexaSet.Rdash.class.1) (Rfn.[,AlignedRead,ANY,ANY,ANY.Rdash.method)] >> endobj 1947 0 obj << /Names [(Rfn.[,AlignedRead,ANY,ANY.Rdash.method) 409 0 R (Rfn.[,AlignedRead,ANY,missing,ANY.Rdash.method) 410 0 R (Rfn.[,AlignedRead,ANY,missing.Rdash.method) 411 0 R (Rfn.[,AlignedRead,missing,ANY,ANY.Rdash.method) 412 0 R (Rfn.[,AlignedRead,missing,ANY.Rdash.method) 413 0 R (Rfn.[,AlignedRead,missing,missing,ANY.Rdash.method) 414 0 R] /Limits [(Rfn.[,AlignedRead,ANY,ANY.Rdash.method) (Rfn.[,AlignedRead,missing,missing,ANY.Rdash.method)] >> endobj 1948 0 obj << /Names [(Rfn.[,AlignedRead,missing,missing.Rdash.method) 415 0 R (Rfn.[,IntensityMeasure,ANY,ANY,ANY.Rdash.method) 618 0 R (Rfn.[,IntensityMeasure,ANY,ANY.Rdash.method) 619 0 R (Rfn.[,IntensityMeasure,ANY,missing,ANY.Rdash.method) 620 0 R (Rfn.[,IntensityMeasure,missing,ANY,ANY.Rdash.method) 621 0 R (Rfn.[,IntensityMeasure,missing,missing,ANY.Rdash.method) 622 0 R] /Limits [(Rfn.[,AlignedRead,missing,missing.Rdash.method) (Rfn.[,IntensityMeasure,missing,missing,ANY.Rdash.method)] >> endobj 1949 0 obj << /Names [(Rfn.[,MatrixQuality,ANY,missing,ANY.Rdash.method) 756 0 R (Rfn.[,MatrixQuality,ANY,missing.Rdash.method) 757 0 R (Rfn.[,QualityScore,ANY,missing,ANY.Rdash.method) 758 0 R (Rfn.[,QualityScore,ANY,missing.Rdash.method) 759 0 R (Rfn.[,SRList,ANY,missing,ANY.Rdash.method) 1454 0 R (Rfn.[,SRList,ANY,missing.Rdash.method) 1455 0 R] /Limits [(Rfn.[,MatrixQuality,ANY,missing,ANY.Rdash.method) (Rfn.[,SRList,ANY,missing.Rdash.method)] >> endobj 1950 0 obj << /Names [(Rfn.[,ShortRead,ANY,ANY,ANY.Rdash.method) 1073 0 R (Rfn.[,ShortRead,ANY,ANY.Rdash.method) 1074 0 R (Rfn.[,ShortRead,ANY,missing,ANY.Rdash.method) 1075 0 R (Rfn.[,ShortRead,ANY,missing.Rdash.method) 1076 0 R (Rfn.[,ShortRead,missing,ANY,ANY.Rdash.method) 1077 0 R (Rfn.[,ShortRead,missing,ANY.Rdash.method) 1078 0 R] /Limits [(Rfn.[,ShortRead,ANY,ANY,ANY.Rdash.method) (Rfn.[,ShortRead,missing,ANY.Rdash.method)] >> endobj 1951 0 obj << /Names [(Rfn.[,ShortRead,missing,missing,ANY.Rdash.method) 1079 0 R (Rfn.[,ShortRead,missing,missing.Rdash.method) 1080 0 R (Rfn.[,ShortReadQ,ANY,ANY,ANY.Rdash.method) 1130 0 R (Rfn.[,ShortReadQ,ANY,ANY.Rdash.method) 1131 0 R (Rfn.[,ShortReadQ,ANY,missing,ANY.Rdash.method) 1132 0 R (Rfn.[,ShortReadQ,ANY,missing.Rdash.method) 1133 0 R] /Limits [(Rfn.[,ShortRead,missing,missing,ANY.Rdash.method) (Rfn.[,ShortReadQ,ANY,missing.Rdash.method)] >> endobj 1952 0 obj << /Names [(Rfn.[,ShortReadQ,missing,ANY,ANY.Rdash.method) 1134 0 R (Rfn.[,ShortReadQ,missing,ANY.Rdash.method) 1135 0 R (Rfn.[,ShortReadQ,missing,missing,ANY.Rdash.method) 1136 0 R (Rfn.[,ShortReadQ,missing,missing.Rdash.method) 1137 0 R (Rfn.[,SolexaIntensity,ANY,ANY,ANY.Rdash.method) 1179 0 R (Rfn.[,SolexaIntensity,ANY,ANY.Rdash.method) 1180 0 R] /Limits [(Rfn.[,ShortReadQ,missing,ANY,ANY.Rdash.method) (Rfn.[,SolexaIntensity,ANY,ANY.Rdash.method)] >> endobj 1953 0 obj << /Names [(Rfn.[,SolexaIntensity,ANY,missing,ANY.Rdash.method) 1181 0 R (Rfn.[,SolexaIntensity,missing,ANY,ANY.Rdash.method) 1182 0 R (Rfn.[,SolexaIntensity,missing,missing,ANY.Rdash.method) 1183 0 R (Rfn.[[,ArrayIntensity,ANY,ANY.Rdash.method) 623 0 R (Rfn.[[,MatrixQuality,ANY,missing.Rdash.method) 760 0 R (Rfn.[[,QualityScore,ANY,missing.Rdash.method) 761 0 R] /Limits [(Rfn.[,SolexaIntensity,ANY,missing,ANY.Rdash.method) (Rfn.[[,QualityScore,ANY,missing.Rdash.method)] >> endobj 1954 0 obj << /Names [(Rfn.[[,SRList,ANY,missing.Rdash.method) 1456 0 R (Rfn.accessors) 312 0 R (Rfn.accessors.1) 6 0 R (Rfn.alignData) 315 0 R (Rfn.alignDataFilter) 1364 0 R (Rfn.alignQuality) 316 0 R] /Limits [(Rfn.[[,SRList,ANY,missing.Rdash.method) (Rfn.alignQuality)] >> endobj 1955 0 obj << /Names [(Rfn.alignQualityFilter) 1365 0 R (Rfn.alphabet,FastqQuality.Rdash.method) 725 0 R (Rfn.alphabetByCycle) 445 0 R (Rfn.alphabetByCycle,BStringSet.Rdash.method) 446 0 R (Rfn.alphabetByCycle,FastqQuality.Rdash.method) 726 0 R (Rfn.alphabetByCycle,ShortRead.Rdash.method) 1054 0 R] /Limits [(Rfn.alignQualityFilter) (Rfn.alphabetByCycle,ShortRead.Rdash.method)] >> endobj 1956 0 obj << /Names [(Rfn.alphabetByCycle,ShortReadQ.Rdash.method) 1121 0 R (Rfn.alphabetByCycle.1) 26 0 R (Rfn.alphabetFrequency) 784 0 R (Rfn.alphabetFrequency,FastqQuality.Rdash.method) 727 0 R (Rfn.alphabetScore) 474 0 R (Rfn.alphabetScore,FastqQuality.Rdash.method) 728 0 R] /Limits [(Rfn.alphabetByCycle,ShortReadQ.Rdash.method) (Rfn.alphabetScore,FastqQuality.Rdash.method)] >> endobj 1957 0 obj << /Names [(Rfn.alphabetScore,SFastqQuality.Rdash.method) 729 0 R (Rfn.alphabetScore,ShortReadQ.Rdash.method) 1122 0 R (Rfn.alphabetScore.1) 30 0 R (Rfn.analysisPath) 317 0 R (Rfn.append,.ShortReadBase,.ShortReadBase,ANY.Rdash.method) 1102 0 R (Rfn.append,AlignedDataFrame,AlignedDataFrame,missing.Rdash.method) 364 0 R] /Limits [(Rfn.alphabetScore,SFastqQuality.Rdash.method) (Rfn.append,AlignedDataFrame,AlignedDataFrame,missing.Rdash.method)] >> endobj 1958 0 obj << /Names [(Rfn.append,AlignedRead,AlignedRead,missing.Rdash.method) 399 0 R (Rfn.append,MatrixQuality,MatrixQuality,missing.Rdash.method) 730 0 R (Rfn.append,QualityScore,QualityScore,missing.Rdash.method) 731 0 R (Rfn.append,ShortRead,ShortRead,missing.Rdash.method) 1055 0 R (Rfn.append,ShortReadQ,ShortReadQ,missing.Rdash.method) 1123 0 R (Rfn.baseCallPath) 318 0 R] /Limits [(Rfn.append,AlignedRead,AlignedRead,missing.Rdash.method) (Rfn.baseCallPath)] >> endobj 1959 0 obj << /Names [(Rfn.basePath) 529 0 R (Rfn.chromosome) 319 0 R (Rfn.chromosomeFilter) 1366 0 R (Rfn.clean) 499 0 R (Rfn.clean,DNAStringSet.Rdash.method) 500 0 R (Rfn.clean,ShortRead.Rdash.method) 1056 0 R] /Limits [(Rfn.basePath) (Rfn.clean,ShortRead.Rdash.method)] >> endobj 1960 0 obj << /Names [(Rfn.clean.1) 38 0 R (Rfn.coerce,FastqQuality,matrix.Rdash.method) 732 0 R (Rfn.coerce,FastqQuality,numeric.Rdash.method) 733 0 R (Rfn.coerce,PairwiseAlignedXStringSet,AlignedRead.Rdash.method) 400 0 R (Rfn.coerce,SFastqQuality,matrix.Rdash.method) 734 0 R (Rfn.compose) 1367 0 R] /Limits [(Rfn.clean.1) (Rfn.compose)] >> endobj 1961 0 obj << /Names [(Rfn.countLines) 513 0 R (Rfn.countLines.1) 42 0 R (Rfn.coverage,AlignedRead.Rdash.method) 401 0 R (Rfn.dataPath) 320 0 R (Rfn.deprecated) 528 0 R (Rfn.deprecated.1) 46 0 R] /Limits [(Rfn.countLines) (Rfn.deprecated.1)] >> endobj 1962 0 obj << /Names [(Rfn.detail) 534 0 R (Rfn.detail,.ShortReadBase.Rdash.method) 1436 0 R (Rfn.detail,AlignedRead.Rdash.method) 402 0 R (Rfn.detail,ExperimentPath.Rdash.method) 568 0 R (Rfn.detail,QualityScore.Rdash.method) 735 0 R (Rfn.detail,RochePath.Rdash.method) 988 0 R] /Limits [(Rfn.detail) (Rfn.detail,RochePath.Rdash.method)] >> endobj 1963 0 obj << /Names [(Rfn.detail,SRList.Rdash.method) 1437 0 R (Rfn.detail,SRSet.Rdash.method) 1407 0 R (Rfn.detail,SRVector.Rdash.method) 1438 0 R (Rfn.detail,ShortRead.Rdash.method) 1057 0 R (Rfn.detail,ShortReadQ.Rdash.method) 1124 0 R (Rfn.detail,SolexaPath.Rdash.method) 1227 0 R] /Limits [(Rfn.detail,SRList.Rdash.method) (Rfn.detail,SolexaPath.Rdash.method)] >> endobj 1964 0 obj << /Names [(Rfn.detail,SolexaSet.Rdash.method) 1264 0 R (Rfn.detail.1) 50 0 R (Rfn.dim,Intensity.Rdash.method) 610 0 R (Rfn.dim,MatrixQuality.Rdash.method) 736 0 R (Rfn.dustyFilter) 1368 0 R (Rfn.dustyScore) 547 0 R] /Limits [(Rfn.detail,SolexaSet.Rdash.method) (Rfn.dustyScore)] >> endobj 1965 0 obj << /Names [(Rfn.dustyScore,DNAStringSet.Rdash.method) 548 0 R (Rfn.dustyScore,ShortRead.Rdash.method) 549 0 R (Rfn.dustyScore.1) 54 0 R (Rfn.experimentPath) 321 0 R (Rfn.experimentPath,SRSet.Rdash.method) 1408 0 R (Rfn.function.Rdash.class) 1379 0 R] /Limits [(Rfn.dustyScore,DNAStringSet.Rdash.method) (Rfn.function.Rdash.class)] >> endobj 1966 0 obj << /Names [(Rfn.grep) 520 0 R (Rfn.id) 322 0 R (Rfn.idFilter) 1369 0 R (Rfn.imageAnalysisPath) 323 0 R (Rfn.intensity) 611 0 R (Rfn.is) 1461 0 R] /Limits [(Rfn.grep) (Rfn.is)] >> endobj 1967 0 obj << /Names [(Rfn.laneDescription) 324 0 R (Rfn.laneNames) 325 0 R (Rfn.laneNames,AnnotatedDataFrame.Rdash.method) 1265 0 R (Rfn.laneNames,SolexaSet.Rdash.method) 1266 0 R (Rfn.lapply) 1471 0 R (Rfn.lapply,SRList,ANY.Rdash.method) 1439 0 R] /Limits [(Rfn.laneDescription) (Rfn.lapply,SRList,ANY.Rdash.method)] >> endobj 1968 0 obj << /Names [(Rfn.lapply,SRList.Rdash.method) 1440 0 R (Rfn.length,MatrixQuality.Rdash.method) 739 0 R (Rfn.length,QualityScore.Rdash.method) 740 0 R (Rfn.length,SRList.Rdash.method) 1441 0 R (Rfn.length,ShortRead.Rdash.method) 1058 0 R (Rfn.list.files) 521 0 R] /Limits [(Rfn.lapply,SRList.Rdash.method) (Rfn.list.files)] >> endobj 1969 0 obj << /Names [(Rfn.measurementError) 614 0 R (Rfn.nFilter) 1370 0 R (Rfn.name) 1341 0 R (Rfn.name,SRFilter.Rdash.method) 1342 0 R (Rfn.names,SRList.Rdash.method) 1442 0 R (Rfn.names<.Rdash.,SRList,character.Rdash.method) 1443 0 R] /Limits [(Rfn.measurementError) (Rfn.names<.Rdash.,SRList,character.Rdash.method)] >> endobj 1970 0 obj << /Names [(Rfn.narrow) 785 0 R (Rfn.narrow,FastqQuality.Rdash.method) 742 0 R (Rfn.narrow,MatrixQuality.Rdash.method) 743 0 R (Rfn.narrow,ShortRead.Rdash.method) 1059 0 R (Rfn.narrow,ShortReadQ.Rdash.method) 1125 0 R (Rfn.pairwiseAlignment) 1308 0 R] /Limits [(Rfn.narrow) (Rfn.pairwiseAlignment)] >> endobj 1971 0 obj << /Names [(Rfn.phenoData,SRSet.Rdash.method) 1409 0 R (Rfn.phenoData.Rdash.class) 1429 0 R (Rfn.pileup) 661 0 R (Rfn.pileup.1) 74 0 R (Rfn.polyn) 675 0 R (Rfn.polynFilter) 1371 0 R] /Limits [(Rfn.phenoData,SRSet.Rdash.method) (Rfn.polynFilter)] >> endobj 1972 0 obj << /Names [(Rfn.position) 326 0 R (Rfn.positionFilter) 1372 0 R (Rfn.qa) 487 0 R (Rfn.qa,SolexaPath.Rdash.method) 1228 0 R (Rfn.qa,character.Rdash.method) 708 0 R (Rfn.qa.1) 86 0 R] /Limits [(Rfn.position) (Rfn.qa.1)] >> endobj 1973 0 obj << /Names [(Rfn.qualPath) 989 0 R (Rfn.rank) 1330 0 R (Rfn.read454) 990 0 R (Rfn.read454,RochePath.Rdash.method) 991 0 R (Rfn.readAligned) 422 0 R (Rfn.readAligned,SolexaPath.Rdash.method) 1229 0 R] /Limits [(Rfn.qualPath) (Rfn.readAligned,SolexaPath.Rdash.method)] >> endobj 1974 0 obj << /Names [(Rfn.readAligned,SolexaSet.Rdash.method) 1267 0 R (Rfn.readAligned,character.Rdash.method) 820 0 R (Rfn.readAligned.1) 98 0 R (Rfn.readBaseQuality) 864 0 R (Rfn.readBaseQuality,SolexaPath.Rdash.method) 1230 0 R (Rfn.readBaseQuality,character.Rdash.method) 865 0 R] /Limits [(Rfn.readAligned,SolexaSet.Rdash.method) (Rfn.readBaseQuality,character.Rdash.method)] >> endobj 1975 0 obj << /Names [(Rfn.readBaseQuality.1) 102 0 R (Rfn.readBfaToc) 666 0 R (Rfn.readBfaToc.1) 106 0 R (Rfn.readCount) 1410 0 R (Rfn.readData) 1411 0 R (Rfn.readFasta) 992 0 R] /Limits [(Rfn.readBaseQuality.1) (Rfn.readFasta)] >> endobj 1976 0 obj << /Names [(Rfn.readFasta,RochePath.Rdash.method) 994 0 R (Rfn.readFasta,character.Rdash.method) 993 0 R (Rfn.readFastq) 813 0 R (Rfn.readFastq,SolexaPath.Rdash.method) 1231 0 R (Rfn.readFastq,character.Rdash.method) 890 0 R (Rfn.readFastq.1) 110 0 R] /Limits [(Rfn.readFasta,RochePath.Rdash.method) (Rfn.readFastq.1)] >> endobj 1977 0 obj << /Names [(Rfn.readIndex) 1412 0 R (Rfn.readInfo) 615 0 R (Rfn.readIntensities) 631 0 R (Rfn.readIntensities,SolexaPath.Rdash.method) 1232 0 R (Rfn.readIntensities,character.Rdash.method) 914 0 R (Rfn.readIntensities.1) 114 0 R] /Limits [(Rfn.readIndex) (Rfn.readIntensities.1)] >> endobj 1978 0 obj << /Names [(Rfn.readPath) 995 0 R (Rfn.readPrb) 885 0 R (Rfn.readPrb,SolexaPath.Rdash.method) 1233 0 R (Rfn.readPrb,character.Rdash.method) 928 0 R (Rfn.readPrb.1) 118 0 R (Rfn.readQseq) 943 0 R] /Limits [(Rfn.readPath) (Rfn.readQseq)] >> endobj 1979 0 obj << /Names [(Rfn.readQseq,SolexaPath.Rdash.method) 1234 0 R (Rfn.readQseq,character.Rdash.method) 944 0 R (Rfn.readQseq.1) 122 0 R (Rfn.readQual) 996 0 R (Rfn.readQual,RochePath.Rdash.method) 998 0 R (Rfn.readQual,character.Rdash.method) 997 0 R] /Limits [(Rfn.readQseq,SolexaPath.Rdash.method) (Rfn.readQual,character.Rdash.method)] >> endobj 1980 0 obj << /Names [(Rfn.readXStringColumns) 838 0 R (Rfn.readXStringColumns.1) 126 0 R (Rfn.report) 717 0 R (Rfn.report,ANY.Rdash.method) 972 0 R (Rfn.report,BowtieQA.Rdash.method) 481 0 R (Rfn.report,FastqQA.Rdash.method) 591 0 R] /Limits [(Rfn.readXStringColumns) (Rfn.report,FastqQA.Rdash.method)] >> endobj 1981 0 obj << /Names [(Rfn.report,MAQMapQA.Rdash.method) 648 0 R (Rfn.report,SolexaExportQA.Rdash.method) 1159 0 R (Rfn.report,SolexaPath.Rdash.method) 1235 0 R (Rfn.report.1) 130 0 R (Rfn.runNames) 1002 0 R (Rfn.runNames,RochePath.Rdash.method) 1003 0 R] /Limits [(Rfn.report,MAQMapQA.Rdash.method) (Rfn.runNames,RochePath.Rdash.method)] >> endobj 1982 0 obj << /Names [(Rfn.sapply) 1472 0 R (Rfn.sapply,SRList.Rdash.method) 1444 0 R (Rfn.scanPath) 327 0 R (Rfn.show) 540 0 R (Rfn.show,.QA.Rdash.method) 1160 0 R (Rfn.show,.ShortReadBase.Rdash.method) 1103 0 R] /Limits [(Rfn.sapply) (Rfn.show,.ShortReadBase.Rdash.method)] >> endobj 1983 0 obj << /Names [(Rfn.show,AlignedRead.Rdash.method) 403 0 R (Rfn.show,ExperimentPath.Rdash.method) 570 0 R (Rfn.show,FastqQuality.Rdash.method) 746 0 R (Rfn.show,Intensity.Rdash.method) 616 0 R (Rfn.show,IntensityMeasure.Rdash.method) 617 0 R (Rfn.show,NumericQuality.Rdash.method) 747 0 R] /Limits [(Rfn.show,AlignedRead.Rdash.method) (Rfn.show,NumericQuality.Rdash.method)] >> endobj 1984 0 obj << /Names [(Rfn.show,RochePath.Rdash.method) 1004 0 R (Rfn.show,SRFilter.Rdash.method) 1343 0 R (Rfn.show,SRList.Rdash.method) 1445 0 R (Rfn.show,SRSet.Rdash.method) 1413 0 R (Rfn.show,SRVector.Rdash.method) 1446 0 R (Rfn.show,ShortRead.Rdash.method) 1064 0 R] /Limits [(Rfn.show,RochePath.Rdash.method) (Rfn.show,ShortRead.Rdash.method)] >> endobj 1985 0 obj << /Names [(Rfn.show,SolexaExportQA.Rdash.method) 1161 0 R (Rfn.show,SolexaPath.Rdash.method) 1236 0 R (Rfn.show,SolexaSet.Rdash.method) 1268 0 R (Rfn.solexaPath) 328 0 R (Rfn.sourcePath) 1414 0 R (Rfn.sprintf) 1460 0 R] /Limits [(Rfn.show,SolexaExportQA.Rdash.method) (Rfn.sprintf)] >> endobj 1986 0 obj << /Names [(Rfn.srFilter) 1363 0 R (Rfn.srFilter,SRFilter.Rdash.method) 1344 0 R (Rfn.srFilter,function.Rdash.method) 1374 0 R (Rfn.srFilter,missing.Rdash.method) 1375 0 R (Rfn.srFilter.1) 190 0 R (Rfn.srapply) 934 0 R] /Limits [(Rfn.srFilter) (Rfn.srapply)] >> endobj 1987 0 obj << /Names [(Rfn.srapply.1) 174 0 R (Rfn.srdistance) 1105 0 R (Rfn.srdistance,DNAStringSet,DNAString.Rdash.method) 1301 0 R (Rfn.srdistance,DNAStringSet,DNAStringSet.Rdash.method) 1302 0 R (Rfn.srdistance,DNAStringSet,character.Rdash.method) 1300 0 R (Rfn.srdistance,ShortRead,ANY.Rdash.method) 1065 0 R] /Limits [(Rfn.srapply.1) (Rfn.srdistance,ShortRead,ANY.Rdash.method)] >> endobj 1988 0 obj << /Names [(Rfn.srdistance.1) 178 0 R (Rfn.srdistanceFilter) 1373 0 R (Rfn.srduplicated) 1319 0 R (Rfn.srduplicated,AlignedRead.Rdash.method) 404 0 R (Rfn.srduplicated,FastqQuality.Rdash.method) 748 0 R (Rfn.srduplicated,ShortRead.Rdash.method) 1066 0 R] /Limits [(Rfn.srdistance.1) (Rfn.srduplicated,ShortRead.Rdash.method)] >> endobj 1989 0 obj << /Names [(Rfn.srduplicated,XStringSet.Rdash.method) 1320 0 R (Rfn.srduplicated.1) 182 0 R (Rfn.sread) 329 0 R (Rfn.srorder) 1321 0 R (Rfn.srorder,AlignedRead.Rdash.method) 405 0 R (Rfn.srorder,FastqQuality.Rdash.method) 749 0 R] /Limits [(Rfn.srduplicated,XStringSet.Rdash.method) (Rfn.srorder,FastqQuality.Rdash.method)] >> endobj 1990 0 obj << /Names [(Rfn.srorder,ShortRead.Rdash.method) 1067 0 R (Rfn.srorder,XStringSet.Rdash.method) 1322 0 R (Rfn.srrank) 1323 0 R (Rfn.srrank,AlignedRead.Rdash.method) 406 0 R (Rfn.srrank,FastqQuality.Rdash.method) 750 0 R (Rfn.srrank,ShortRead.Rdash.method) 1068 0 R] /Limits [(Rfn.srorder,ShortRead.Rdash.method) (Rfn.srrank,ShortRead.Rdash.method)] >> endobj 1991 0 obj << /Names [(Rfn.srrank,XStringSet.Rdash.method) 1324 0 R (Rfn.srsort) 786 0 R (Rfn.srsort,FastqQuality.Rdash.method) 751 0 R (Rfn.srsort,ShortRead.Rdash.method) 1069 0 R (Rfn.srsort,XStringSet.Rdash.method) 1325 0 R (Rfn.strand,AlignedRead.Rdash.method) 407 0 R] /Limits [(Rfn.srrank,XStringSet.Rdash.method) (Rfn.strand,AlignedRead.Rdash.method)] >> endobj 1992 0 obj << /Names [(Rfn.strandFilter) 1376 0 R (Rfn.tables) 1108 0 R (Rfn.tables,ShortRead.Rdash.method) 1070 0 R (Rfn.tables,XStringSet.Rdash.method) 1478 0 R (Rfn.tables.1) 202 0 R (Rfn.trimLRPatterns) 1106 0 R] /Limits [(Rfn.strandFilter) (Rfn.trimLRPatterns)] >> endobj 1993 0 obj << /Names [(Rfn.trimLRPatterns,ShortRead.Rdash.method) 1071 0 R (Rfn.uniqueFilter) 1377 0 R (Rfn.vclass) 330 0 R (Rfn.width,FastqQuality.Rdash.method) 752 0 R (Rfn.width,MatrixQuality.Rdash.method) 753 0 R (Rfn.width,NumericQuality.Rdash.method) 754 0 R] /Limits [(Rfn.trimLRPatterns,ShortRead.Rdash.method) (Rfn.width,NumericQuality.Rdash.method)] >> endobj 1994 0 obj << /Names [(Rfn.width,QualityScore.Rdash.method) 755 0 R (Rfn.width,ShortRead.Rdash.method) 1072 0 R (Rfn.writeFastq) 891 0 R (Rfn.writeFastq,ShortReadQ.Rdash.method) 1129 0 R (chapter*.1) 253 0 R (index.0) 206 0 R] /Limits [(Rfn.width,QualityScore.Rdash.method) (index.0)] >> endobj 1995 0 obj << /Names [(page.1) 251 0 R (page.10) 266 0 R (page.11) 267 0 R (page.12) 268 0 R (page.13) 269 0 R (page.14) 270 0 R] /Limits [(page.1) (page.14)] >> endobj 1996 0 obj << /Names [(page.15) 271 0 R (page.16) 272 0 R (page.17) 273 0 R (page.18) 274 0 R (page.19) 275 0 R (page.2) 259 0 R] /Limits [(page.15) (page.2)] >> endobj 1997 0 obj << /Names [(page.20) 276 0 R (page.21) 277 0 R (page.22) 278 0 R (page.23) 780 0 R (page.24) 279 0 R (page.25) 280 0 R] /Limits [(page.20) (page.25)] >> endobj 1998 0 obj << /Names [(page.26) 836 0 R (page.27) 843 0 R (page.28) 853 0 R (page.29) 281 0 R (page.3) 260 0 R (page.30) 282 0 R] /Limits [(page.26) (page.30)] >> endobj 1999 0 obj << /Names [(page.31) 283 0 R (page.32) 902 0 R (page.33) 284 0 R (page.34) 285 0 R (page.35) 286 0 R (page.36) 287 0 R] /Limits [(page.31) (page.36)] >> endobj 2000 0 obj << /Names [(page.37) 288 0 R (page.38) 289 0 R (page.39) 1017 0 R (page.4) 261 0 R (page.40) 290 0 R (page.41) 291 0 R] /Limits [(page.37) (page.41)] >> endobj 2001 0 obj << /Names [(page.42) 292 0 R (page.43) 293 0 R (page.44) 333 0 R (page.45) 334 0 R (page.46) 1200 0 R (page.47) 335 0 R] /Limits [(page.42) (page.47)] >> endobj 2002 0 obj << /Names [(page.48) 336 0 R (page.49) 1251 0 R (page.5) 262 0 R (page.50) 337 0 R (page.51) 1280 0 R (page.52) 338 0 R] /Limits [(page.48) (page.52)] >> endobj 2003 0 obj << /Names [(page.53) 339 0 R (page.54) 340 0 R (page.55) 341 0 R (page.56) 342 0 R (page.57) 1387 0 R (page.58) 1396 0 R] /Limits [(page.53) (page.58)] >> endobj 2004 0 obj << /Names [(page.59) 343 0 R (page.6) 263 0 R (page.60) 1422 0 R (page.61) 344 0 R (page.62) 1467 0 R (page.63) 345 0 R] /Limits [(page.59) (page.63)] >> endobj 2005 0 obj << /Names [(page.64) 1487 0 R (page.65) 346 0 R (page.66) 1618 0 R (page.67) 1678 0 R (page.68) 1740 0 R (page.69) 1802 0 R] /Limits [(page.64) (page.69)] >> endobj 2006 0 obj << /Names [(page.7) 264 0 R (page.70) 1865 0 R (page.71) 1895 0 R (page.8) 456 0 R (page.9) 265 0 R (section*.10) 366 0 R] /Limits [(page.7) (section*.10)] >> endobj 2007 0 obj << /Names [(section*.100) 597 0 R (section*.101) 598 0 R (section*.102) 599 0 R (section*.103) 624 0 R (section*.104) 625 0 R (section*.105) 626 0 R] /Limits [(section*.100) (section*.105)] >> endobj 2008 0 obj << /Names [(section*.106) 627 0 R (section*.107) 628 0 R (section*.108) 643 0 R (section*.109) 644 0 R (section*.11) 367 0 R (section*.110) 645 0 R] /Limits [(section*.106) (section*.110)] >> endobj 2009 0 obj << /Names [(section*.111) 649 0 R (section*.112) 650 0 R (section*.113) 651 0 R (section*.114) 652 0 R (section*.115) 653 0 R (section*.116) 658 0 R] /Limits [(section*.111) (section*.116)] >> endobj 2010 0 obj << /Names [(section*.117) 659 0 R (section*.118) 660 0 R (section*.119) 662 0 R (section*.12) 378 0 R (section*.120) 663 0 R (section*.121) 664 0 R] /Limits [(section*.117) (section*.121)] >> endobj 2011 0 obj << /Names [(section*.122) 665 0 R (section*.123) 670 0 R (section*.124) 671 0 R (section*.125) 673 0 R (section*.126) 676 0 R (section*.127) 677 0 R] /Limits [(section*.122) (section*.127)] >> endobj 2012 0 obj << /Names [(section*.128) 685 0 R (section*.129) 686 0 R (section*.13) 379 0 R (section*.130) 687 0 R (section*.131) 688 0 R (section*.132) 689 0 R] /Limits [(section*.128) (section*.132)] >> endobj 2013 0 obj << /Names [(section*.133) 690 0 R (section*.134) 691 0 R (section*.135) 692 0 R (section*.136) 693 0 R (section*.137) 694 0 R (section*.138) 695 0 R] /Limits [(section*.133) (section*.138)] >> endobj 2014 0 obj << /Names [(section*.139) 696 0 R (section*.14) 380 0 R (section*.140) 709 0 R (section*.141) 710 0 R (section*.142) 711 0 R (section*.143) 712 0 R] /Limits [(section*.139) (section*.143)] >> endobj 2015 0 obj << /Names [(section*.144) 713 0 R (section*.145) 714 0 R (section*.146) 715 0 R (section*.147) 716 0 R (section*.148) 762 0 R (section*.149) 763 0 R] /Limits [(section*.144) (section*.149)] >> endobj 2016 0 obj << /Names [(section*.15) 381 0 R (section*.150) 764 0 R (section*.151) 765 0 R (section*.152) 781 0 R (section*.153) 782 0 R (section*.154) 783 0 R] /Limits [(section*.15) (section*.154)] >> endobj 2017 0 obj << /Names [(section*.155) 805 0 R (section*.156) 806 0 R (section*.157) 807 0 R (section*.158) 808 0 R (section*.159) 809 0 R (section*.16) 382 0 R] /Limits [(section*.155) (section*.16)] >> endobj 2018 0 obj << /Names [(section*.160) 810 0 R (section*.161) 811 0 R (section*.162) 821 0 R (section*.163) 822 0 R (section*.164) 823 0 R (section*.165) 824 0 R] /Limits [(section*.160) (section*.165)] >> endobj 2019 0 obj << /Names [(section*.166) 854 0 R (section*.167) 855 0 R (section*.168) 856 0 R (section*.169) 863 0 R (section*.17) 383 0 R (section*.170) 866 0 R] /Limits [(section*.166) (section*.170)] >> endobj 2020 0 obj << /Names [(section*.171) 867 0 R (section*.172) 868 0 R (section*.173) 869 0 R (section*.174) 877 0 R (section*.175) 878 0 R (section*.176) 879 0 R] /Limits [(section*.171) (section*.176)] >> endobj 2021 0 obj << /Names [(section*.177) 880 0 R (section*.178) 881 0 R (section*.179) 882 0 R (section*.18) 384 0 R (section*.180) 883 0 R (section*.181) 884 0 R] /Limits [(section*.177) (section*.181)] >> endobj 2022 0 obj << /Names [(section*.182) 892 0 R (section*.183) 893 0 R (section*.184) 894 0 R (section*.185) 895 0 R (section*.186) 903 0 R (section*.187) 904 0 R] /Limits [(section*.182) (section*.187)] >> endobj 2023 0 obj << /Names [(section*.188) 905 0 R (section*.189) 906 0 R (section*.19) 385 0 R (section*.190) 915 0 R (section*.191) 916 0 R (section*.192) 917 0 R] /Limits [(section*.188) (section*.192)] >> endobj 2024 0 obj << /Names [(section*.193) 918 0 R (section*.194) 919 0 R (section*.195) 920 0 R (section*.196) 927 0 R (section*.197) 929 0 R (section*.198) 930 0 R] /Limits [(section*.193) (section*.198)] >> endobj 2025 0 obj << /Names [(section*.199) 931 0 R (section*.2) 257 0 R (section*.20) 386 0 R (section*.200) 932 0 R (section*.201) 933 0 R (section*.202) 941 0 R] /Limits [(section*.199) (section*.202)] >> endobj 2026 0 obj << /Names [(section*.203) 942 0 R (section*.204) 945 0 R (section*.205) 946 0 R (section*.206) 947 0 R (section*.207) 948 0 R (section*.208) 949 0 R] /Limits [(section*.203) (section*.208)] >> endobj 2027 0 obj << /Names [(section*.209) 950 0 R (section*.21) 416 0 R (section*.210) 955 0 R (section*.211) 956 0 R (section*.212) 957 0 R (section*.213) 958 0 R] /Limits [(section*.209) (section*.213)] >> endobj 2028 0 obj << /Names [(section*.214) 970 0 R (section*.215) 971 0 R (section*.216) 973 0 R (section*.217) 974 0 R (section*.218) 975 0 R (section*.219) 976 0 R] /Limits [(section*.214) (section*.219)] >> endobj 2029 0 obj << /Names [(section*.22) 417 0 R (section*.220) 983 0 R (section*.221) 984 0 R (section*.222) 985 0 R (section*.223) 986 0 R (section*.224) 1005 0 R] /Limits [(section*.22) (section*.224)] >> endobj 2030 0 obj << /Names [(section*.225) 1006 0 R (section*.226) 1018 0 R (section*.227) 1019 0 R (section*.228) 1020 0 R (section*.229) 1021 0 R (section*.23) 418 0 R] /Limits [(section*.225) (section*.23)] >> endobj 2031 0 obj << /Names [(section*.230) 1022 0 R (section*.231) 1037 0 R (section*.232) 1039 0 R (section*.233) 1040 0 R (section*.234) 1041 0 R (section*.235) 1042 0 R] /Limits [(section*.230) (section*.235)] >> endobj 2032 0 obj << /Names [(section*.236) 1043 0 R (section*.237) 1044 0 R (section*.238) 1045 0 R (section*.239) 1046 0 R (section*.24) 419 0 R (section*.240) 1081 0 R] /Limits [(section*.236) (section*.240)] >> endobj 2033 0 obj << /Names [(section*.241) 1082 0 R (section*.242) 1083 0 R (section*.243) 1084 0 R (section*.244) 1085 0 R (section*.245) 1097 0 R 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