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(Rfn.RangedData) 570 0 R (Rfn.Ranges) 572 0 R (Rfn.RangesList) 569 0 R (Rfn.RochePath) 1406 0 R] /Limits [(Rfn.QualityScore.Rdash.class) (Rfn.RochePath)] >> endobj 2941 0 obj << /Names [(Rfn.RochePath.Rdash.class) 1392 0 R (Rfn.RochePath.Rdash.class.1) 150 0 R (Rfn.RocheSet) 1440 0 R (Rfn.RocheSet,RochePath.Rdash.method) 1408 0 R (Rfn.RocheSet,character.Rdash.method) 1407 0 R (Rfn.RocheSet.Rdash.class) 1428 0 R] /Limits [(Rfn.RochePath.Rdash.class) (Rfn.RocheSet.Rdash.class)] >> endobj 2942 0 obj << /Names [(Rfn.RocheSet.Rdash.class.1) 154 0 R (Rfn.RtaIntensity) 1458 0 R (Rfn.RtaIntensity.1) 158 0 R (Rfn.RtaIntensity.Rdash.class) 1466 0 R (Rfn.RtaIntensity.Rdash.class.1) 162 0 R (Rfn.SFastqQuality) 1062 0 R] /Limits [(Rfn.RocheSet.Rdash.class.1) (Rfn.SFastqQuality)] >> endobj 2943 0 obj << /Names [(Rfn.SFastqQuality,BStringSet.Rdash.method) 1063 0 R (Rfn.SFastqQuality,character.Rdash.method) 1064 0 R (Rfn.SFastqQuality,missing.Rdash.method) 1065 0 R (Rfn.SFastqQuality.Rdash.class) 1106 0 R (Rfn.SRError) 2113 0 R (Rfn.SRError.Rdash.class) 2114 0 R] /Limits [(Rfn.SFastqQuality,BStringSet.Rdash.method) (Rfn.SRError.Rdash.class)] >> endobj 2944 0 obj << /Names [(Rfn.SRFilter.Rdash.class) 1170 0 R (Rfn.SRFilter.Rdash.class.1) 234 0 R (Rfn.SRFilterResult) 2044 0 R (Rfn.SRFilterResult.Rdash.class) 2039 0 R (Rfn.SRFilterResult.Rdash.class.1) 238 0 R (Rfn.SRList) 2115 0 R] /Limits [(Rfn.SRFilter.Rdash.class) (Rfn.SRList)] >> endobj 2945 0 obj << /Names [(Rfn.SRList.Rdash.class) 623 0 R (Rfn.SRSet.Rdash.class) 1449 0 R (Rfn.SRSet.Rdash.class.1) 242 0 R (Rfn.SRUtil.Rdash.class) 2101 0 R (Rfn.SRUtil.Rdash.class.1) 246 0 R (Rfn.SRVector) 2116 0 R] /Limits [(Rfn.SRList.Rdash.class) (Rfn.SRVector)] >> endobj 2946 0 obj << /Names [(Rfn.SRVector.Rdash.class) 2117 0 R (Rfn.SRWarn) 2118 0 R (Rfn.SRWarn.Rdash.class) 2119 0 R (Rfn.ScanBamParam) 1193 0 R (Rfn.ShortRead) 1498 0 R (Rfn.ShortRead,DNAStringSet,BStringSet.Rdash.method) 1499 0 R] /Limits [(Rfn.SRVector.Rdash.class) (Rfn.ShortRead,DNAStringSet,BStringSet.Rdash.method)] >> endobj 2947 0 obj << /Names [(Rfn.ShortRead,DNAStringSet,missing.Rdash.method) 1500 0 R (Rfn.ShortRead,missing,missing.Rdash.method) 1501 0 R (Rfn.ShortRead.Rdash.class) 559 0 R (Rfn.ShortRead.Rdash.class.1) 166 0 R (Rfn.ShortRead.Rdash.deprecated) 1553 0 R (Rfn.ShortRead.Rdash.deprecated.1) 170 0 R] /Limits [(Rfn.ShortRead,DNAStringSet,missing.Rdash.method) (Rfn.ShortRead.Rdash.deprecated.1)] >> endobj 2948 0 obj << /Names [(Rfn.ShortReadBase.Rdash.package) 406 0 R (Rfn.ShortReadBase.Rdash.package.1) 2 0 R (Rfn.ShortReadFile.Rdash.class) 764 0 R (Rfn.ShortReadQ) 1033 0 R (Rfn.ShortReadQ,DNAStringSet,BStringSet,BStringSet.Rdash.method) 1566 0 R (Rfn.ShortReadQ,DNAStringSet,BStringSet,missing.Rdash.method) 1567 0 R] /Limits [(Rfn.ShortReadBase.Rdash.package) (Rfn.ShortReadQ,DNAStringSet,BStringSet,missing.Rdash.method)] >> endobj 2949 0 obj << /Names [(Rfn.ShortReadQ,DNAStringSet,QualityScore,BStringSet.Rdash.method) 1568 0 R (Rfn.ShortReadQ,DNAStringSet,QualityScore,missing.Rdash.method) 1569 0 R (Rfn.ShortReadQ,missing,missing,missing.Rdash.method) 1570 0 R (Rfn.ShortReadQ.Rdash.class) 474 0 R (Rfn.ShortReadQ.Rdash.class.1) 174 0 R (Rfn.ShortReadQA.Rdash.class) 1610 0 R] /Limits [(Rfn.ShortReadQ,DNAStringSet,QualityScore,BStringSet.Rdash.method) (Rfn.ShortReadQA.Rdash.class)] >> endobj 2950 0 obj << /Names [(Rfn.ShortReadQA.Rdash.class.1) 178 0 R (Rfn.ShortReadQQA.Rdash.class) 1615 0 R (Rfn.Snapshot) 1652 0 R (Rfn.Snapshot,BamFileList,GRanges.Rdash.method) 1653 0 R (Rfn.Snapshot,character,GRanges.Rdash.method) 1654 0 R (Rfn.Snapshot,character,missing.Rdash.method) 1655 0 R] /Limits [(Rfn.ShortReadQA.Rdash.class.1) (Rfn.Snapshot,character,missing.Rdash.method)] >> endobj 2951 0 obj << /Names [(Rfn.Snapshot.Rdash.class) 1636 0 R (Rfn.Snapshot.Rdash.class.1) 182 0 R (Rfn.SnapshotFunction) 1705 0 R (Rfn.SnapshotFunction.Rdash.class) 1701 0 R (Rfn.SnapshotFunction.Rdash.class.1) 186 0 R (Rfn.SnapshotFunctionList) 1679 0 R] /Limits [(Rfn.Snapshot.Rdash.class) (Rfn.SnapshotFunctionList)] >> endobj 2952 0 obj << /Names [(Rfn.SnapshotFunctionList,ANY.Rdash.method) 1706 0 R (Rfn.SnapshotFunctionList,SnapshotFunction.Rdash.method) 1707 0 R (Rfn.SnapshotFunctionList.Rdash.class) 1708 0 R (Rfn.SolexaExportQA) 1734 0 R (Rfn.SolexaExportQA.Rdash.class) 927 0 R (Rfn.SolexaExportQA.Rdash.class.1) 190 0 R] /Limits [(Rfn.SnapshotFunctionList,ANY.Rdash.method) (Rfn.SolexaExportQA.Rdash.class.1)] >> endobj 2953 0 obj << /Names [(Rfn.SolexaIntensity) 858 0 R (Rfn.SolexaIntensity.1) 194 0 R (Rfn.SolexaIntensity.Rdash.class) 857 0 R (Rfn.SolexaIntensity.Rdash.class.1) 198 0 R (Rfn.SolexaIntensityInfo) 1754 0 R (Rfn.SolexaIntensityInfo.Rdash.class) 1758 0 R] /Limits [(Rfn.SolexaIntensity) (Rfn.SolexaIntensityInfo.Rdash.class)] >> endobj 2954 0 obj << /Names [(Rfn.SolexaPath) 908 0 R (Rfn.SolexaPath.Rdash.class) 734 0 R (Rfn.SolexaPath.Rdash.class.1) 202 0 R (Rfn.SolexaRealignQA.Rdash.class) 1735 0 R (Rfn.SolexaSet) 1857 0 R (Rfn.SolexaSet,SolexaPath.Rdash.method) 1812 0 R] /Limits [(Rfn.SolexaPath) (Rfn.SolexaSet,SolexaPath.Rdash.method)] >> endobj 2955 0 obj << /Names [(Rfn.SolexaSet,character.Rdash.method) 1858 0 R (Rfn.SolexaSet.Rdash.class) 1180 0 R (Rfn.SolexaSet.Rdash.class.1) 206 0 R (Rfn.SpTrellis) 1690 0 R (Rfn.SpTrellis.Rdash.class) 1871 0 R (Rfn.SpTrellis.Rdash.class.1) 210 0 R] /Limits [(Rfn.SolexaSet,character.Rdash.method) (Rfn.SpTrellis.Rdash.class.1)] >> endobj 2956 0 obj << /Names [(Rfn.Utilites) 2192 0 R (Rfn.Utilites.1) 258 0 R (Rfn.Versioned) 498 0 R (Rfn.XStringSet) 598 0 R (Rfn.[,AlignedRead,ANY,ANY,ANY.Rdash.method) 546 0 R (Rfn.[,AlignedRead,ANY,ANY.Rdash.method) 547 0 R] /Limits [(Rfn.Utilites) (Rfn.[,AlignedRead,ANY,ANY.Rdash.method)] >> endobj 2957 0 obj << /Names [(Rfn.[,AlignedRead,ANY,missing,ANY.Rdash.method) 548 0 R (Rfn.[,AlignedRead,ANY,missing.Rdash.method) 549 0 R (Rfn.[,AlignedRead,missing,ANY,ANY.Rdash.method) 550 0 R (Rfn.[,AlignedRead,missing,ANY.Rdash.method) 551 0 R (Rfn.[,AlignedRead,missing,missing,ANY.Rdash.method) 552 0 R (Rfn.[,AlignedRead,missing,missing.Rdash.method) 553 0 R] /Limits [(Rfn.[,AlignedRead,ANY,missing,ANY.Rdash.method) (Rfn.[,AlignedRead,missing,missing.Rdash.method)] >> endobj 2958 0 obj << /Names [(Rfn.[,IntensityMeasure,ANY,ANY,ANY.Rdash.method) 847 0 R (Rfn.[,IntensityMeasure,ANY,ANY.Rdash.method) 848 0 R (Rfn.[,IntensityMeasure,ANY,missing,ANY.Rdash.method) 849 0 R (Rfn.[,IntensityMeasure,missing,ANY,ANY.Rdash.method) 850 0 R (Rfn.[,IntensityMeasure,missing,missing,ANY.Rdash.method) 851 0 R (Rfn.[,MatrixQuality,ANY,missing,ANY.Rdash.method) 1119 0 R] /Limits [(Rfn.[,IntensityMeasure,ANY,ANY,ANY.Rdash.method) (Rfn.[,MatrixQuality,ANY,missing,ANY.Rdash.method)] >> endobj 2959 0 obj << /Names [(Rfn.[,MatrixQuality,ANY,missing.Rdash.method) 1120 0 R (Rfn.[,QualityScore,ANY,missing,ANY.Rdash.method) 1121 0 R (Rfn.[,QualityScore,ANY,missing.Rdash.method) 1122 0 R (Rfn.[,SRList,ANY,missing,ANY.Rdash.method) 2120 0 R (Rfn.[,SRList,ANY,missing.Rdash.method) 2121 0 R (Rfn.[,ShortRead,ANY,ANY,ANY.Rdash.method) 1512 0 R] /Limits [(Rfn.[,MatrixQuality,ANY,missing.Rdash.method) (Rfn.[,ShortRead,ANY,ANY,ANY.Rdash.method)] >> endobj 2960 0 obj << /Names [(Rfn.[,ShortRead,ANY,ANY.Rdash.method) 1513 0 R (Rfn.[,ShortRead,ANY,missing,ANY.Rdash.method) 1514 0 R (Rfn.[,ShortRead,ANY,missing.Rdash.method) 1515 0 R (Rfn.[,ShortRead,missing,ANY,ANY.Rdash.method) 1516 0 R (Rfn.[,ShortRead,missing,ANY.Rdash.method) 1517 0 R (Rfn.[,ShortRead,missing,missing,ANY.Rdash.method) 1518 0 R] /Limits [(Rfn.[,ShortRead,ANY,ANY.Rdash.method) (Rfn.[,ShortRead,missing,missing,ANY.Rdash.method)] >> endobj 2961 0 obj << /Names [(Rfn.[,ShortRead,missing,missing.Rdash.method) 1519 0 R (Rfn.[,ShortReadQ,ANY,ANY,ANY.Rdash.method) 1575 0 R (Rfn.[,ShortReadQ,ANY,ANY.Rdash.method) 1576 0 R (Rfn.[,ShortReadQ,ANY,missing,ANY.Rdash.method) 1577 0 R (Rfn.[,ShortReadQ,ANY,missing.Rdash.method) 1578 0 R (Rfn.[,ShortReadQ,missing,ANY,ANY.Rdash.method) 1579 0 R] /Limits [(Rfn.[,ShortRead,missing,missing.Rdash.method) (Rfn.[,ShortReadQ,missing,ANY,ANY.Rdash.method)] >> endobj 2962 0 obj << /Names [(Rfn.[,ShortReadQ,missing,ANY.Rdash.method) 1580 0 R (Rfn.[,ShortReadQ,missing,missing,ANY.Rdash.method) 1581 0 R (Rfn.[,ShortReadQ,missing,missing.Rdash.method) 1582 0 R (Rfn.[,SolexaIntensity,ANY,ANY,ANY.Rdash.method) 1770 0 R (Rfn.[,SolexaIntensity,ANY,ANY.Rdash.method) 1771 0 R (Rfn.[,SolexaIntensity,ANY,missing,ANY.Rdash.method) 1772 0 R] /Limits [(Rfn.[,ShortReadQ,missing,ANY.Rdash.method) (Rfn.[,SolexaIntensity,ANY,missing,ANY.Rdash.method)] >> endobj 2963 0 obj << /Names [(Rfn.[,SolexaIntensity,missing,ANY,ANY.Rdash.method) 1773 0 R (Rfn.[,SolexaIntensity,missing,missing,ANY.Rdash.method) 1774 0 R (Rfn.[[,ArrayIntensity,ANY,ANY.Rdash.method) 852 0 R (Rfn.[[,MatrixQuality,ANY,missing.Rdash.method) 1123 0 R (Rfn.[[,QualityScore,ANY,missing.Rdash.method) 1124 0 R (Rfn.[[,SRList,ANY,missing.Rdash.method) 2122 0 R] /Limits [(Rfn.[,SolexaIntensity,missing,ANY,ANY.Rdash.method) (Rfn.[[,SRList,ANY,missing.Rdash.method)] >> endobj 2964 0 obj << /Names [(Rfn.accessors) 441 0 R (Rfn.accessors.1) 10 0 R (Rfn.alignData) 442 0 R (Rfn.alignDataFilter) 1967 0 R (Rfn.alignQuality) 443 0 R (Rfn.alignQualityFilter) 1968 0 R] /Limits [(Rfn.accessors) (Rfn.alignQualityFilter)] >> endobj 2965 0 obj << /Names [(Rfn.alphabet,FastqQuality.Rdash.method) 1082 0 R (Rfn.alphabetByCycle) 581 0 R (Rfn.alphabetByCycle,BStringSet.Rdash.method) 582 0 R (Rfn.alphabetByCycle,FastqQuality.Rdash.method) 1083 0 R (Rfn.alphabetByCycle,ShortRead.Rdash.method) 1491 0 R (Rfn.alphabetByCycle,ShortReadQ.Rdash.method) 1559 0 R] /Limits [(Rfn.alphabet,FastqQuality.Rdash.method) (Rfn.alphabetByCycle,ShortReadQ.Rdash.method)] >> endobj 2966 0 obj << /Names [(Rfn.alphabetByCycle.1) 30 0 R (Rfn.alphabetFrequency) 1146 0 R (Rfn.alphabetFrequency,FastqQuality.Rdash.method) 1084 0 R (Rfn.alphabetScore) 609 0 R (Rfn.alphabetScore,FastqQuality.Rdash.method) 1085 0 R (Rfn.alphabetScore,SFastqQuality.Rdash.method) 1086 0 R] /Limits [(Rfn.alphabetByCycle.1) (Rfn.alphabetScore,SFastqQuality.Rdash.method)] >> endobj 2967 0 obj << /Names [(Rfn.alphabetScore,ShortReadQ.Rdash.method) 1560 0 R (Rfn.alphabetScore.1) 34 0 R (Rfn.analysisPath) 444 0 R (Rfn.annTrack) 1637 0 R (Rfn.annTrack,Snapshot.Rdash.method) 1638 0 R (Rfn.append,.ShortReadBase,.ShortReadBase.Rdash.method) 411 0 R] /Limits [(Rfn.alphabetScore,ShortReadQ.Rdash.method) (Rfn.append,.ShortReadBase,.ShortReadBase.Rdash.method)] >> endobj 2968 0 obj << /Names [(Rfn.append,AlignedDataFrame,AlignedDataFrame.Rdash.method) 490 0 R (Rfn.append,AlignedRead,AlignedRead.Rdash.method) 530 0 R (Rfn.append,MatrixQuality,MatrixQuality.Rdash.method) 1087 0 R (Rfn.append,QualityScore,QualityScore.Rdash.method) 1088 0 R (Rfn.append,ShortRead,ShortRead.Rdash.method) 1492 0 R (Rfn.append,ShortReadQ,ShortReadQ.Rdash.method) 1561 0 R] /Limits [(Rfn.append,AlignedDataFrame,AlignedDataFrame.Rdash.method) (Rfn.append,ShortReadQ,ShortReadQ.Rdash.method)] >> endobj 2969 0 obj << /Names [(Rfn.atomic) 2069 0 R (Rfn.baseCallPath) 445 0 R (Rfn.basePath) 683 0 R (Rfn.c,GappedReads.Rdash.method) 807 0 R (Rfn.c,SRFilter.Rdash.method) 2014 0 R (Rfn.chromosome) 446 0 R] /Limits [(Rfn.atomic) (Rfn.chromosome)] >> endobj 2970 0 obj << /Names [(Rfn.chromosome,AlignedRead.Rdash.method) 531 0 R (Rfn.chromosomeFilter) 1969 0 R (Rfn.class:GappedReads) 808 0 R (Rfn.clean) 655 0 R (Rfn.clean,DNAStringSet.Rdash.method) 656 0 R (Rfn.clean,ShortRead.Rdash.method) 1493 0 R] /Limits [(Rfn.chromosome,AlignedRead.Rdash.method) (Rfn.clean,ShortRead.Rdash.method)] >> endobj 2971 0 obj << /Names [(Rfn.clean.1) 46 0 R (Rfn.close.ShortReadFile) 740 0 R (Rfn.coerce,AlignedRead,GAlignments.Rdash.method) 532 0 R (Rfn.coerce,AlignedRead,GRanges.Rdash.method) 534 0 R (Rfn.coerce,AlignedRead,GappedReads.Rdash.method) 533 0 R (Rfn.coerce,AlignedRead,RangedData.Rdash.method) 535 0 R] /Limits [(Rfn.clean.1) (Rfn.coerce,AlignedRead,RangedData.Rdash.method)] >> endobj 2972 0 obj << /Names [(Rfn.coerce,AlignedRead,RangesList.Rdash.method) 536 0 R (Rfn.coerce,FastqQuality,PhredQuality.Rdash.method) 1091 0 R (Rfn.coerce,FastqQuality,matrix.Rdash.method) 1089 0 R (Rfn.coerce,FastqQuality,numeric.Rdash.method) 1090 0 R (Rfn.coerce,PairwiseAlignments,AlignedRead.Rdash.method) 537 0 R (Rfn.coerce,SFastqQuality,SolexaQuality.Rdash.method) 1093 0 R] /Limits [(Rfn.coerce,AlignedRead,RangesList.Rdash.method) (Rfn.coerce,SFastqQuality,SolexaQuality.Rdash.method)] >> endobj 2973 0 obj << /Names [(Rfn.coerce,SFastqQuality,matrix.Rdash.method) 1092 0 R (Rfn.coerce,SRFilter,FilterRules.Rdash.method) 2015 0 R (Rfn.coerce,ShortReadQ,QualityScaledDNAStringSet.Rdash.method) 1562 0 R (Rfn.compose) 1970 0 R (Rfn.countLines) 669 0 R (Rfn.countLines.1) 50 0 R] /Limits [(Rfn.coerce,SFastqQuality,matrix.Rdash.method) (Rfn.countLines.1)] >> endobj 2974 0 obj << /Names [(Rfn.coverage) 1237 0 R (Rfn.coverage,AlignedRead.Rdash.method) 538 0 R (Rfn.data.frame) 1740 0 R (Rfn.dataPath) 447 0 R (Rfn.defunct) 684 0 R (Rfn.deprecated) 682 0 R] /Limits [(Rfn.coverage) (Rfn.deprecated)] >> endobj 2975 0 obj << /Names [(Rfn.deprecated.1) 54 0 R (Rfn.detail,.ShortReadBase.Rdash.method) 2102 0 R (Rfn.detail,AlignedRead.Rdash.method) 539 0 R (Rfn.detail,ExperimentPath.Rdash.method) 723 0 R (Rfn.detail,QualityScore.Rdash.method) 1094 0 R (Rfn.detail,RochePath.Rdash.method) 1393 0 R] /Limits [(Rfn.deprecated.1) (Rfn.detail,RochePath.Rdash.method)] >> endobj 2976 0 obj << /Names [(Rfn.detail,SRList.Rdash.method) 2103 0 R (Rfn.detail,SRSet.Rdash.method) 2080 0 R (Rfn.detail,SRVector.Rdash.method) 2104 0 R (Rfn.detail,ShortRead.Rdash.method) 1494 0 R (Rfn.detail,ShortReadQ.Rdash.method) 1563 0 R (Rfn.detail,SolexaPath.Rdash.method) 1801 0 R] /Limits [(Rfn.detail,SRList.Rdash.method) (Rfn.detail,SolexaPath.Rdash.method)] >> endobj 2977 0 obj << /Names [(Rfn.detail,SolexaSet.Rdash.method) 1852 0 R (Rfn.dim,Intensity.Rdash.method) 839 0 R (Rfn.dim,MatrixQuality.Rdash.method) 1095 0 R (Rfn.dustyFilter) 1971 0 R (Rfn.dustyScore) 697 0 R (Rfn.dustyScore,DNAStringSet.Rdash.method) 698 0 R] /Limits [(Rfn.detail,SolexaSet.Rdash.method) (Rfn.dustyScore,DNAStringSet.Rdash.method)] >> endobj 2978 0 obj << /Names [(Rfn.dustyScore,ShortRead.Rdash.method) 699 0 R (Rfn.dustyScore.1) 58 0 R (Rfn.encoding,FastqQuality.Rdash.method) 1096 0 R (Rfn.encoding,SFastqQuality.Rdash.method) 1097 0 R (Rfn.experimentPath) 448 0 R (Rfn.experimentPath,SRSet.Rdash.method) 2081 0 R] /Limits [(Rfn.dustyScore,ShortRead.Rdash.method) (Rfn.experimentPath,SRSet.Rdash.method)] >> endobj 2979 0 obj << /Names [(Rfn.fac) 1639 0 R (Rfn.fac,Snapshot.Rdash.method) 1640 0 R (Rfn.files) 1641 0 R (Rfn.files,Snapshot.Rdash.method) 1642 0 R (Rfn.filterFastq) 791 0 R (Rfn.filterFastq.1) 70 0 R] /Limits [(Rfn.fac) (Rfn.filterFastq.1)] >> endobj 2980 0 obj << /Names [(Rfn.flag) 982 0 R (Rfn.flag,.QA2.Rdash.method) 983 0 R (Rfn.flag,QAFrequentSequence.Rdash.method) 984 0 R (Rfn.flag,QAReadQuality.Rdash.method) 985 0 R (Rfn.flag,QASource.Rdash.method) 986 0 R (Rfn.function) 1739 0 R] /Limits [(Rfn.flag) (Rfn.function)] >> endobj 2981 0 obj << /Names [(Rfn.function.Rdash.class) 2048 0 R (Rfn.functions) 1643 0 R (Rfn.functions,Snapshot.Rdash.method) 1644 0 R (Rfn.getTrellis) 1645 0 R (Rfn.getTrellis,Snapshot.Rdash.method) 1646 0 R (Rfn.grep) 676 0 R] /Limits [(Rfn.function.Rdash.class) (Rfn.grep)] >> endobj 2982 0 obj << /Names [(Rfn.id) 449 0 R (Rfn.id,ShortRead.Rdash.method) 1495 0 R (Rfn.idFilter) 1972 0 R (Rfn.ignore.strand) 1647 0 R (Rfn.ignore.strand,Snapshot.Rdash.method) 1648 0 R (Rfn.imageAnalysisPath) 450 0 R] /Limits [(Rfn.id) (Rfn.imageAnalysisPath)] >> endobj 2983 0 obj << /Names [(Rfn.intensity) 840 0 R (Rfn.is) 2134 0 R (Rfn.laneDescription) 451 0 R (Rfn.laneNames) 452 0 R (Rfn.laneNames,AnnotatedDataFrame.Rdash.method) 1853 0 R (Rfn.laneNames,SolexaSet.Rdash.method) 1854 0 R] /Limits [(Rfn.intensity) (Rfn.laneNames,SolexaSet.Rdash.method)] >> endobj 2984 0 obj << /Names [(Rfn.lapply) 2145 0 R (Rfn.lapply,SRList,ANY.Rdash.method) 2105 0 R (Rfn.lapply,SRList.Rdash.method) 2106 0 R (Rfn.left,SpTrellis.Rdash.method) 1872 0 R (Rfn.length,MatrixQuality.Rdash.method) 1100 0 R (Rfn.length,QualityScore.Rdash.method) 1101 0 R] /Limits [(Rfn.lapply) (Rfn.length,QualityScore.Rdash.method)] >> endobj 2985 0 obj << /Names [(Rfn.length,SRList.Rdash.method) 2107 0 R (Rfn.length,ShortRead.Rdash.method) 1496 0 R (Rfn.limits) 1702 0 R (Rfn.list.files) 677 0 R (Rfn.logical.Rdash.class) 2067 0 R (Rfn.matchPattern) 1034 0 R] /Limits [(Rfn.length,SRList.Rdash.method) (Rfn.matchPattern)] >> endobj 2986 0 obj << /Names [(Rfn.measurementError) 843 0 R (Rfn.nFilter) 1973 0 R (Rfn.name) 2016 0 R (Rfn.name,SRFilter.Rdash.method) 2017 0 R (Rfn.name,SRFilterResult.Rdash.method) 2042 0 R (Rfn.names,SRList.Rdash.method) 2108 0 R] /Limits [(Rfn.measurementError) (Rfn.names,SRList.Rdash.method)] >> endobj 2987 0 obj << /Names [(Rfn.names<.Rdash.,SRList,character.Rdash.method) 2109 0 R (Rfn.narrow) 1147 0 R (Rfn.narrow,FastqQuality.Rdash.method) 1103 0 R (Rfn.narrow,GappedReads.Rdash.method) 810 0 R (Rfn.narrow,MatrixQuality.Rdash.method) 1104 0 R (Rfn.narrow,ShortRead.Rdash.method) 1497 0 R] /Limits [(Rfn.names<.Rdash.,SRList,character.Rdash.method) (Rfn.narrow,ShortRead.Rdash.method)] >> endobj 2988 0 obj << /Names [(Rfn.narrow,ShortReadQ.Rdash.method) 1564 0 R (Rfn.occurrenceFilter) 1974 0 R (Rfn.open.ShortReadFile) 762 0 R (Rfn.overlap) 573 0 R (Rfn.pairwiseAlignment) 1938 0 R (Rfn.pan) 1649 0 R] /Limits [(Rfn.narrow,ShortReadQ.Rdash.method) (Rfn.pan)] >> endobj 2989 0 obj << /Names [(Rfn.pan,Snapshot.Rdash.method) 1650 0 R (Rfn.phenoData,SRSet.Rdash.method) 2082 0 R (Rfn.phenoData.Rdash.class) 2124 0 R (Rfn.pileup) 685 0 R (Rfn.polyn) 2193 0 R (Rfn.polynFilter) 1975 0 R] /Limits [(Rfn.pan,Snapshot.Rdash.method) (Rfn.polynFilter)] >> endobj 2990 0 obj << /Names [(Rfn.position) 453 0 R (Rfn.position,AlignedRead.Rdash.method) 540 0 R (Rfn.positionFilter) 1976 0 R (Rfn.qa) 433 0 R (Rfn.qa,ShortReadQ.Rdash.method) 1565 0 R (Rfn.qa,SolexaPath.Rdash.method) 1802 0 R] /Limits [(Rfn.position) (Rfn.qa,SolexaPath.Rdash.method)] >> endobj 2991 0 obj << /Names [(Rfn.qa,character.Rdash.method) 902 0 R (Rfn.qa,list.Rdash.method) 903 0 R (Rfn.qa.1) 86 0 R (Rfn.qa2) 965 0 R (Rfn.qa2,FastqSampler.Rdash.method) 988 0 R (Rfn.qa2,QAAdapterContamination.Rdash.method) 989 0 R] /Limits [(Rfn.qa,character.Rdash.method) (Rfn.qa2,QAAdapterContamination.Rdash.method)] >> endobj 2992 0 obj << /Names [(Rfn.qa2,QACollate.Rdash.method) 990 0 R (Rfn.qa2,QAFastqSource.Rdash.method) 991 0 R (Rfn.qa2,QAFrequentSequence.Rdash.method) 992 0 R (Rfn.qa2,QANucleotideByCycle.Rdash.method) 993 0 R (Rfn.qa2,QANucleotideUse.Rdash.method) 994 0 R (Rfn.qa2,QAQualityByCycle.Rdash.method) 995 0 R] /Limits [(Rfn.qa2,QACollate.Rdash.method) (Rfn.qa2,QAQualityByCycle.Rdash.method)] >> endobj 2993 0 obj << /Names [(Rfn.qa2,QAQualityUse.Rdash.method) 996 0 R (Rfn.qa2,QAReadQuality.Rdash.method) 997 0 R (Rfn.qa2,QASequenceUse.Rdash.method) 998 0 R (Rfn.qa2.1) 94 0 R (Rfn.qnarrow,GappedReads.Rdash.method) 811 0 R (Rfn.qseq) 812 0 R] /Limits [(Rfn.qa2,QAQualityUse.Rdash.method) (Rfn.qseq)] >> endobj 2994 0 obj << /Names [(Rfn.qseq,GappedReads.Rdash.method) 813 0 R (Rfn.qualPath) 1394 0 R (Rfn.qwidth,GappedReads.Rdash.method) 814 0 R (Rfn.rank) 1957 0 R (Rfn.rbind) 1044 0 R (Rfn.rbind,.QA.Rdash.method) 417 0 R] /Limits [(Rfn.qseq,GappedReads.Rdash.method) (Rfn.rbind,.QA.Rdash.method)] >> endobj 2995 0 obj << /Names [(Rfn.rbind,QASummary.Rdash.method) 1004 0 R (Rfn.read454) 1395 0 R (Rfn.read454,RochePath.Rdash.method) 1396 0 R (Rfn.readAligned) 516 0 R (Rfn.readAligned,SolexaPath.Rdash.method) 1803 0 R (Rfn.readAligned,SolexaSet.Rdash.method) 1855 0 R] /Limits [(Rfn.rbind,QASummary.Rdash.method) (Rfn.readAligned,SolexaSet.Rdash.method)] >> endobj 2996 0 obj << /Names [(Rfn.readAligned,character.Rdash.method) 1157 0 R (Rfn.readAligned.1) 106 0 R (Rfn.readBaseQuality) 1217 0 R (Rfn.readBaseQuality,RochePath.Rdash.method) 1397 0 R (Rfn.readBaseQuality,SolexaPath.Rdash.method) 1804 0 R (Rfn.readBaseQuality,character.Rdash.method) 1218 0 R] /Limits [(Rfn.readAligned,character.Rdash.method) (Rfn.readBaseQuality,character.Rdash.method)] >> endobj 2997 0 obj << /Names [(Rfn.readBaseQuality.1) 110 0 R (Rfn.readBfaToc) 691 0 R (Rfn.readBfaToc.1) 114 0 R (Rfn.readCount) 2083 0 R (Rfn.readData) 2084 0 R (Rfn.readFasta) 1245 0 R] /Limits [(Rfn.readBaseQuality.1) (Rfn.readFasta)] >> endobj 2998 0 obj << /Names [(Rfn.readFasta,RochePath.Rdash.method) 1398 0 R (Rfn.readFasta,SolexaPath.Rdash.method) 1805 0 R (Rfn.readFasta,character.Rdash.method) 1246 0 R (Rfn.readFasta.1) 118 0 R (Rfn.readFastaQual) 1399 0 R (Rfn.readFastaQual,RochePath.Rdash.method) 1401 0 R] /Limits [(Rfn.readFasta,RochePath.Rdash.method) (Rfn.readFastaQual,RochePath.Rdash.method)] >> endobj 2999 0 obj << /Names [(Rfn.readFastaQual,character.Rdash.method) 1400 0 R (Rfn.readFastq) 786 0 R (Rfn.readFastq,FastqFile.Rdash.method) 763 0 R (Rfn.readFastq,SolexaPath.Rdash.method) 1806 0 R (Rfn.readFastq,character.Rdash.method) 1261 0 R (Rfn.readFastq.1) 122 0 R] /Limits [(Rfn.readFastaQual,character.Rdash.method) (Rfn.readFastq.1)] >> endobj 3000 0 obj << /Names [(Rfn.readGAlignments) 819 0 R (Rfn.readGappedReads) 815 0 R (Rfn.readGappedReadsFromBam) 820 0 R (Rfn.readIndex) 2085 0 R (Rfn.readInfo) 844 0 R (Rfn.readIntensities) 859 0 R] /Limits [(Rfn.readGAlignments) (Rfn.readIntensities)] >> endobj 3001 0 obj << /Names [(Rfn.readIntensities,SolexaPath.Rdash.method) 1807 0 R (Rfn.readIntensities,character.Rdash.method) 1283 0 R (Rfn.readIntensities.1) 126 0 R (Rfn.readIntensities\\unhbox\040\\voidb@x\040\\kern\040\\z@\040\\char\040`\\protect\040\\relax\040\\kern\040.16667em\040character.Rdash.method) 1831 0 R (Rfn.readPath) 1402 0 R (Rfn.readPrb) 1236 0 R] /Limits [(Rfn.readIntensities,SolexaPath.Rdash.method) (Rfn.readPrb)] >> endobj 3002 0 obj << /Names [(Rfn.readPrb,SolexaPath.Rdash.method) 1808 0 R (Rfn.readPrb,character.Rdash.method) 1303 0 R (Rfn.readPrb.1) 130 0 R (Rfn.readPrb\\unhbox\040\\voidb@x\040\\kern\040\\z@\040\\char\040`\\protect\040\\relax\040\\kern\040.16667em\040character.Rdash.method) 1832 0 R (Rfn.readQseq) 1317 0 R (Rfn.readQseq,SolexaPath.Rdash.method) 1809 0 R] /Limits [(Rfn.readPrb,SolexaPath.Rdash.method) (Rfn.readQseq,SolexaPath.Rdash.method)] >> endobj 3003 0 obj << /Names [(Rfn.readQseq,character.Rdash.method) 1318 0 R (Rfn.readQseq.1) 134 0 R (Rfn.readQseq\\unhbox\040\\voidb@x\040\\kern\040\\z@\040\\char\040`\\protect\040\\relax\040\\kern\040.16667em\040character.Rdash.method) 1833 0 R (Rfn.readQual) 1403 0 R (Rfn.readQual,RochePath.Rdash.method) 1405 0 R (Rfn.readQual,character.Rdash.method) 1404 0 R] /Limits [(Rfn.readQseq,character.Rdash.method) (Rfn.readQual,character.Rdash.method)] >> endobj 3004 0 obj << /Names [(Rfn.readXStringColumns) 1181 0 R (Rfn.readXStringColumns.1) 138 0 R (Rfn.reader) 1703 0 R (Rfn.renew) 1344 0 R (Rfn.renew,.ShortReadBase.Rdash.method) 1345 0 R (Rfn.renewable) 1343 0 R] /Limits [(Rfn.readXStringColumns) (Rfn.renewable)] >> endobj 3005 0 obj << /Names [(Rfn.renewable,.ShortReadBase.Rdash.method) 1346 0 R (Rfn.renewable,character.Rdash.method) 1347 0 R (Rfn.renewable,missing.Rdash.method) 1348 0 R (Rfn.renewable.1) 142 0 R (Rfn.report) 907 0 R (Rfn.report,ANY.Rdash.method) 1362 0 R] /Limits [(Rfn.renewable,.ShortReadBase.Rdash.method) (Rfn.report,ANY.Rdash.method)] >> endobj 3006 0 obj << /Names [(Rfn.report,BAMQA.Rdash.method) 616 0 R (Rfn.report,BowtieQA.Rdash.method) 641 0 R (Rfn.report,FastqQA.Rdash.method) 1612 0 R (Rfn.report,MAQMapQA.Rdash.method) 886 0 R (Rfn.report,QA.Rdash.method) 1005 0 R (Rfn.report,QAAdapterContamination.Rdash.method) 1006 0 R] /Limits [(Rfn.report,BAMQA.Rdash.method) (Rfn.report,QAAdapterContamination.Rdash.method)] >> endobj 3007 0 obj << /Names [(Rfn.report,QAFiltered.Rdash.method) 1007 0 R (Rfn.report,QAFlagged.Rdash.method) 1008 0 R (Rfn.report,QAFrequentSequence.Rdash.method) 1009 0 R (Rfn.report,QANucleotideByCycle.Rdash.method) 1010 0 R (Rfn.report,QANucleotideUse.Rdash.method) 1011 0 R (Rfn.report,QAQualityByCycle.Rdash.method) 1012 0 R] /Limits [(Rfn.report,QAFiltered.Rdash.method) (Rfn.report,QAQualityByCycle.Rdash.method)] >> endobj 3008 0 obj << /Names [(Rfn.report,QAQualityUse.Rdash.method) 1013 0 R (Rfn.report,QAReadQuality.Rdash.method) 1014 0 R (Rfn.report,QASequenceUse.Rdash.method) 1015 0 R (Rfn.report,QASource.Rdash.method) 1016 0 R (Rfn.report,SolexaExportQA.Rdash.method) 1730 0 R (Rfn.report,SolexaPath.Rdash.method) 1810 0 R] /Limits [(Rfn.report,QAQualityUse.Rdash.method) (Rfn.report,SolexaPath.Rdash.method)] >> endobj 3009 0 obj << /Names [(Rfn.report.1) 146 0 R (Rfn.report.Rul.html) 1363 0 R (Rfn.report.Rul.html,BAMQA.Rdash.method) 617 0 R (Rfn.report.Rul.html,BowtieQA.Rdash.method) 642 0 R (Rfn.report.Rul.html,FastqQA.Rdash.method) 1613 0 R (Rfn.report.Rul.html,MAQMapQA.Rdash.method) 887 0 R] /Limits [(Rfn.report.1) (Rfn.report.Rul.html,MAQMapQA.Rdash.method)] >> endobj 3010 0 obj << /Names [(Rfn.report.Rul.html,ShortReadQQA.Rdash.method) 1614 0 R (Rfn.report.Rul.html,SolexaExportQA.Rdash.method) 1731 0 R (Rfn.report.Rul.html,SolexaRealignQA.Rdash.method) 1732 0 R (Rfn.restore) 1873 0 R (Rfn.restore,SpTrellis.Rdash.method) 1874 0 R (Rfn.right,SpTrellis.Rdash.method) 1875 0 R] /Limits [(Rfn.report.Rul.html,ShortReadQQA.Rdash.method) (Rfn.right,SpTrellis.Rdash.method)] >> endobj 3011 0 obj << /Names [(Rfn.runNames) 1409 0 R (Rfn.runNames,RochePath.Rdash.method) 1410 0 R (Rfn.sapply) 2146 0 R (Rfn.sapply,SRList.Rdash.method) 2110 0 R (Rfn.scanPath) 454 0 R (Rfn.show,.QA.Rdash.method) 418 0 R] /Limits [(Rfn.runNames) (Rfn.show,.QA.Rdash.method)] >> endobj 3012 0 obj << /Names [(Rfn.show,.ShortReadBase.Rdash.method) 412 0 R (Rfn.show,AlignedRead.Rdash.method) 541 0 R (Rfn.show,ExperimentPath.Rdash.method) 725 0 R (Rfn.show,FastqQuality.Rdash.method) 1107 0 R (Rfn.show,Intensity.Rdash.method) 845 0 R (Rfn.show,IntensityMeasure.Rdash.method) 846 0 R] /Limits [(Rfn.show,.ShortReadBase.Rdash.method) (Rfn.show,IntensityMeasure.Rdash.method)] >> endobj 3013 0 obj << /Names [(Rfn.show,NumericQuality.Rdash.method) 1108 0 R (Rfn.show,QAAdapterContamination.Rdash.method) 1017 0 R (Rfn.show,QACollate.Rdash.method) 1018 0 R (Rfn.show,QAFastqSource.Rdash.method) 1019 0 R (Rfn.show,QAFrequentSequence.Rdash.method) 1020 0 R (Rfn.show,QAReadQuality.Rdash.method) 1021 0 R] /Limits [(Rfn.show,NumericQuality.Rdash.method) (Rfn.show,QAReadQuality.Rdash.method)] >> endobj 3014 0 obj << /Names [(Rfn.show,QASummary.Rdash.method) 1022 0 R (Rfn.show,RochePath.Rdash.method) 1411 0 R (Rfn.show,SRFilter.Rdash.method) 2018 0 R (Rfn.show,SRFilterResult.Rdash.method) 2043 0 R (Rfn.show,SRList.Rdash.method) 2111 0 R (Rfn.show,SRSet.Rdash.method) 2086 0 R] /Limits [(Rfn.show,QASummary.Rdash.method) (Rfn.show,SRSet.Rdash.method)] >> endobj 3015 0 obj << /Names [(Rfn.show,SRVector.Rdash.method) 2112 0 R (Rfn.show,ShortRead.Rdash.method) 1502 0 R (Rfn.show,Snapshot.Rdash.method) 1651 0 R (Rfn.show,SnapshotFunction.Rdash.method) 1704 0 R (Rfn.show,SolexaExportQA.Rdash.method) 1733 0 R (Rfn.show,SolexaPath.Rdash.method) 1811 0 R] /Limits [(Rfn.show,SRVector.Rdash.method) (Rfn.show,SolexaPath.Rdash.method)] >> endobj 3016 0 obj << /Names [(Rfn.show,SolexaSet.Rdash.method) 1856 0 R (Rfn.show,SpTrellis.Rdash.method) 1876 0 R (Rfn.solexaPath) 455 0 R (Rfn.sourcePath) 2087 0 R (Rfn.spViewPerFeature) 1900 0 R (Rfn.spViewPerFeature.1) 214 0 R] /Limits [(Rfn.show,SolexaSet.Rdash.method) (Rfn.spViewPerFeature.1)] >> endobj 3017 0 obj << /Names [(Rfn.sprintf) 2133 0 R (Rfn.srFilter) 1273 0 R (Rfn.srFilter,SRFilter.Rdash.method) 2019 0 R (Rfn.srFilter,function.Rdash.method) 1978 0 R (Rfn.srFilter,missing.Rdash.method) 1979 0 R (Rfn.srFilter.1) 230 0 R] /Limits [(Rfn.sprintf) (Rfn.srFilter.1)] >> endobj 3018 0 obj << /Names [(Rfn.srapply) 909 0 R (Rfn.srapply.1) 218 0 R (Rfn.srdistance) 1541 0 R (Rfn.srdistance,DNAStringSet,DNAString.Rdash.method) 1928 0 R (Rfn.srdistance,DNAStringSet,DNAStringSet.Rdash.method) 1929 0 R (Rfn.srdistance,DNAStringSet,character.Rdash.method) 1927 0 R] /Limits [(Rfn.srapply) (Rfn.srdistance,DNAStringSet,character.Rdash.method)] >> endobj 3019 0 obj << /Names [(Rfn.srdistance,ShortRead,ANY.Rdash.method) 1503 0 R (Rfn.srdistance.1) 222 0 R (Rfn.srdistanceFilter) 1977 0 R (Rfn.srduplicated) 1946 0 R (Rfn.srduplicated,AlignedRead.Rdash.method) 542 0 R (Rfn.srduplicated,FastqQuality.Rdash.method) 1109 0 R] /Limits [(Rfn.srdistance,ShortRead,ANY.Rdash.method) (Rfn.srduplicated,FastqQuality.Rdash.method)] >> endobj 3020 0 obj << /Names [(Rfn.srduplicated,ShortRead.Rdash.method) 1504 0 R (Rfn.srduplicated,XStringSet.Rdash.method) 1947 0 R (Rfn.srduplicated.1) 226 0 R (Rfn.sread) 456 0 R (Rfn.sread,ShortRead.Rdash.method) 457 0 R (Rfn.srorder) 1948 0 R] /Limits [(Rfn.srduplicated,ShortRead.Rdash.method) (Rfn.srorder)] >> endobj 3021 0 obj << /Names [(Rfn.srorder,AlignedRead.Rdash.method) 543 0 R (Rfn.srorder,FastqQuality.Rdash.method) 1110 0 R (Rfn.srorder,ShortRead.Rdash.method) 1505 0 R (Rfn.srorder,XStringSet.Rdash.method) 1949 0 R (Rfn.srrank) 1950 0 R (Rfn.srrank,AlignedRead.Rdash.method) 544 0 R] /Limits [(Rfn.srorder,AlignedRead.Rdash.method) (Rfn.srrank,AlignedRead.Rdash.method)] >> endobj 3022 0 obj << /Names [(Rfn.srrank,FastqQuality.Rdash.method) 1111 0 R (Rfn.srrank,ShortRead.Rdash.method) 1506 0 R (Rfn.srrank,XStringSet.Rdash.method) 1951 0 R (Rfn.srsort) 1161 0 R (Rfn.srsort,FastqQuality.Rdash.method) 1112 0 R (Rfn.srsort,ShortRead.Rdash.method) 1507 0 R] /Limits [(Rfn.srrank,FastqQuality.Rdash.method) (Rfn.srsort,ShortRead.Rdash.method)] >> endobj 3023 0 obj << /Names [(Rfn.srsort,XStringSet.Rdash.method) 1952 0 R (Rfn.stats) 2045 0 R (Rfn.stats,SRFilterResult.Rdash.method) 2046 0 R (Rfn.strand,AlignedRead.Rdash.method) 545 0 R (Rfn.strandFilter) 1980 0 R (Rfn.tables) 1543 0 R] /Limits [(Rfn.srsort,XStringSet.Rdash.method) (Rfn.tables)] >> endobj 3024 0 obj << /Names [(Rfn.tables,ShortRead.Rdash.method) 1508 0 R (Rfn.tables,XStringSet.Rdash.method) 2151 0 R (Rfn.tables.1) 250 0 R (Rfn.tapply) 2008 0 R (Rfn.togglefun) 1656 0 R (Rfn.togglefun,Snapshot.Rdash.method) 1657 0 R] /Limits [(Rfn.tables,ShortRead.Rdash.method) (Rfn.togglefun,Snapshot.Rdash.method)] >> endobj 3025 0 obj << /Names [(Rfn.togglep) 1658 0 R (Rfn.togglep,Snapshot.Rdash.method) 1659 0 R (Rfn.togglez) 1660 0 R (Rfn.togglez,Snapshot.Rdash.method) 1661 0 R (Rfn.trellis.Rdash.class) 1662 0 R (Rfn.trimEnds) 2164 0 R] /Limits [(Rfn.togglep) (Rfn.trimEnds)] >> endobj 3026 0 obj << /Names [(Rfn.trimEnds,FastqQuality.Rdash.method) 2166 0 R (Rfn.trimEnds,ShortRead.Rdash.method) 2167 0 R (Rfn.trimEnds,ShortReadQ.Rdash.method) 2168 0 R (Rfn.trimEnds,XStringQuality.Rdash.method) 2169 0 R (Rfn.trimEnds,XStringSet.Rdash.method) 2170 0 R (Rfn.trimEnds,character.Rdash.method) 2165 0 R] /Limits [(Rfn.trimEnds,FastqQuality.Rdash.method) (Rfn.trimEnds,character.Rdash.method)] >> endobj 3027 0 obj << /Names [(Rfn.trimLRPatterns) 1542 0 R (Rfn.trimLRPatterns,ShortRead.Rdash.method) 1509 0 R (Rfn.trimTails) 2163 0 R (Rfn.trimTails,BStringSet.Rdash.method) 2171 0 R (Rfn.trimTails,FastqQuality.Rdash.method) 1113 0 R (Rfn.trimTails,ShortReadQ.Rdash.method) 1571 0 R] /Limits [(Rfn.trimLRPatterns) (Rfn.trimTails,ShortReadQ.Rdash.method)] >> endobj 3028 0 obj << /Names [(Rfn.trimTails,XStringQuality.Rdash.method) 2173 0 R (Rfn.trimTails,character.Rdash.method) 2172 0 R (Rfn.trimTails.1) 254 0 R (Rfn.trimTailw) 2174 0 R (Rfn.trimTailw,BStringSet.Rdash.method) 2175 0 R (Rfn.trimTailw,FastqQuality.Rdash.method) 1114 0 R] /Limits [(Rfn.trimTails,XStringQuality.Rdash.method) (Rfn.trimTailw,FastqQuality.Rdash.method)] >> endobj 3029 0 obj << /Names [(Rfn.trimTailw,ShortReadQ.Rdash.method) 1572 0 R (Rfn.trimTailw,XStringQuality.Rdash.method) 2177 0 R (Rfn.trimTailw,character.Rdash.method) 2176 0 R (Rfn.uniqueFilter) 1554 0 R (Rfn.vclass) 458 0 R (Rfn.vector.Rdash.class) 2068 0 R] /Limits [(Rfn.trimTailw,ShortReadQ.Rdash.method) (Rfn.vector.Rdash.class)] >> endobj 3030 0 obj << /Names [(Rfn.view) 1663 0 R (Rfn.view,Snapshot.Rdash.method) 1664 0 R (Rfn.viewer) 1709 0 R (Rfn.vrange) 1665 0 R (Rfn.vrange,Snapshot.Rdash.method) 1666 0 R (Rfn.width,FastqQuality.Rdash.method) 1115 0 R] /Limits [(Rfn.view) (Rfn.width,FastqQuality.Rdash.method)] >> endobj 3031 0 obj << /Names [(Rfn.width,MatrixQuality.Rdash.method) 1116 0 R (Rfn.width,NumericQuality.Rdash.method) 1117 0 R (Rfn.width,QualityScore.Rdash.method) 1118 0 R (Rfn.width,ShortRead.Rdash.method) 1510 0 R (Rfn.writeFasta) 1247 0 R (Rfn.writeFasta,DNAStringSet.Rdash.method) 1248 0 R] /Limits [(Rfn.width,MatrixQuality.Rdash.method) (Rfn.writeFasta,DNAStringSet.Rdash.method)] >> endobj 3032 0 obj << /Names [(Rfn.writeFasta,ShortRead.Rdash.method) 1511 0 R (Rfn.writeFastq) 787 0 R (Rfn.writeFastq,ShortReadQ,FastqFile.Rdash.method) 1574 0 R (Rfn.writeFastq,ShortReadQ,character.Rdash.method) 1573 0 R (Rfn.writeXStringSet) 1253 0 R (Rfn.yield) 765 0 R] /Limits [(Rfn.writeFasta,ShortRead.Rdash.method) (Rfn.yield)] >> endobj 3033 0 obj << /Names [(Rfn.yield,FastqFileReader.Rdash.method) 766 0 R (Rfn.yield,FastqSampler.Rdash.method) 767 0 R (Rfn.yield,FastqStreamer.Rdash.method) 768 0 R (Rfn.zi) 1877 0 R (Rfn.zi,SpTrellis.Rdash.method) 1878 0 R (Rfn.zo) 1879 0 R] /Limits [(Rfn.yield,FastqFileReader.Rdash.method) (Rfn.zo)] >> endobj 3034 0 obj << /Names [(Rfn.zo,SpTrellis.Rdash.method) 1880 0 R (Rfn.zoom) 1667 0 R (Rfn.zoom,Snapshot.Rdash.method) 1668 0 R (chapter*.1) 281 0 R (index.0) 262 0 R (page.1) 279 0 R] /Limits [(Rfn.zo,SpTrellis.Rdash.method) (page.1)] >> endobj 3035 0 obj << /Names [(page.10) 345 0 R (page.100) 2184 0 R (page.101) 431 0 R (page.102) 2203 0 R (page.103) 432 0 R (page.104) 2329 0 R] /Limits [(page.10) (page.104)] >> endobj 3036 0 obj << /Names [(page.105) 2388 0 R (page.106) 2447 0 R (page.107) 2505 0 R (page.108) 2571 0 R (page.109) 2637 0 R (page.11) 591 0 R] /Limits [(page.105) (page.11)] >> endobj 3037 0 obj << /Names [(page.110) 2701 0 R (page.111) 2759 0 R (page.112) 2824 0 R (page.113) 2879 0 R (page.114) 2890 0 R (page.12) 346 0 R] /Limits [(page.110) (page.12)] >> endobj 3038 0 obj << /Names [(page.13) 347 0 R (page.14) 348 0 R (page.15) 349 0 R (page.16) 350 0 R (page.17) 351 0 R (page.18) 708 0 R] /Limits [(page.13) (page.18)] >> endobj 3039 0 obj << /Names [(page.19) 352 0 R (page.2) 343 0 R (page.20) 353 0 R (page.21) 781 0 R (page.22) 354 0 R (page.23) 355 0 R] /Limits [(page.19) (page.23)] >> endobj 3040 0 obj << /Names [(page.24) 356 0 R (page.25) 865 0 R (page.26) 357 0 R (page.27) 358 0 R (page.28) 921 0 R (page.29) 359 0 R] /Limits [(page.24) (page.29)] >> endobj 3041 0 obj << /Names [(page.3) 288 0 R (page.30) 360 0 R (page.31) 1030 0 R (page.32) 1042 0 R (page.33) 361 0 R (page.34) 362 0 R] /Limits [(page.3) (page.34)] >> endobj 3042 0 obj << /Names [(page.35) 1131 0 R (page.36) 1145 0 R (page.37) 363 0 R (page.38) 1167 0 R (page.39) 1179 0 R (page.4) 289 0 R] /Limits [(page.35) (page.4)] >> endobj 3043 0 obj << /Names [(page.40) 1186 0 R (page.41) 1192 0 R (page.42) 1203 0 R (page.43) 364 0 R (page.44) 365 0 R (page.45) 366 0 R] /Limits [(page.40) (page.45)] >> endobj 3044 0 obj << /Names [(page.46) 367 0 R (page.47) 1270 0 R (page.48) 368 0 R (page.49) 1291 0 R (page.5) 290 0 R (page.50) 369 0 R] /Limits [(page.46) (page.50)] >> endobj 3045 0 obj << /Names [(page.51) 370 0 R (page.52) 371 0 R (page.53) 1335 0 R (page.54) 372 0 R (page.55) 373 0 R (page.56) 1378 0 R] /Limits [(page.51) (page.56)] >> endobj 3046 0 obj << /Names [(page.57) 374 0 R (page.58) 1423 0 R (page.59) 375 0 R (page.6) 291 0 R (page.60) 376 0 R (page.61) 377 0 R] /Limits [(page.57) (page.61)] >> endobj 3047 0 obj << /Names [(page.62) 378 0 R (page.63) 1537 0 R (page.64) 379 0 R (page.65) 1595 0 R (page.66) 380 0 R (page.67) 381 0 R] /Limits [(page.62) (page.67)] >> endobj 3048 0 obj << /Names [(page.68) 1675 0 R (page.69) 1684 0 R (page.7) 292 0 R (page.70) 1694 0 R (page.71) 382 0 R (page.72) 383 0 R] /Limits [(page.68) (page.72)] >> endobj 3049 0 obj << /Names [(page.73) 384 0 R (page.74) 385 0 R (page.75) 1791 0 R (page.76) 386 0 R (page.77) 1827 0 R (page.78) 1839 0 R] /Limits [(page.73) (page.78)] >> endobj 3050 0 obj << /Names [(page.79) 387 0 R (page.8) 293 0 R (page.80) 388 0 R 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