htsworkflow/pipelines/test/testdata/bustard-config132.xml

   1 <?xml version="1.0"?>
   2 <BaseCallAnalysis>
   3   <Run Name="Bustard1.3.2_25-03-2009_diane">
   4     <BaseCallParameters>
   5       <ChastityThreshold>0.600000</ChastityThreshold>
   6       <Matrix Path="/home/diane/gec/090206_HWI-EAS229_0090_311AFAAXX/Data/C1-152_Firecrest1.9.5_14-02-2009_diane/Matrix/s_4_matrix.txt">
   7         <AutoFlag>0</AutoFlag>
   8         <AutoLane>0</AutoLane>
   9         <Cycle>2</Cycle>
  10         <CycleOffset>1</CycleOffset>
  11         <FirstCycle>1</FirstCycle>
  12         <LastCycle>37</LastCycle>
  13         <Read>1</Read>
  14       </Matrix>
  15       <MatrixElements Path="/home/diane/gec/090206_HWI-EAS229_0090_311AFAAXX/Data/C1-152_Firecrest1.9.5_14-02-2009_diane/Matrix/s_4_matrix.txt">
  16         <Base>A</Base>
  17         <Base>C</Base>
  18         <Base>G</Base>
  19         <Base>T</Base>
  20         <Element>1.270000</Element>
  21         <Element>0.210000</Element>
  22         <Element>-0.020000</Element>
  23         <Element>-0.030000</Element>
  24         <Element>0.570000</Element>
  25         <Element>0.580000</Element>
  26         <Element>-0.010000</Element>
  27         <Element>-0.010000</Element>
  28         <Element>-0.030000</Element>
  29         <Element>-0.040000</Element>
  30         <Element>1.510000</Element>
  31         <Element>-0.020000</Element>
  32         <Element>-0.020000</Element>
  33         <Element>-0.020000</Element>
  34         <Element>0.800000</Element>
  35         <Element>1.070000</Element>
  36       </MatrixElements>
  37       <Phasing Path="">
  38         <AutoFlag>1</AutoFlag>
  39         <AutoLane>3</AutoLane>
  40         <Cycle>1</Cycle>
  41         <CycleOffset>0</CycleOffset>
  42         <FirstCycle>1</FirstCycle>
  43         <LastCycle>37</LastCycle>
  44         <Read>1</Read>
  45       </Phasing>
  46       <PhasingRestarts />
  47       <PrbCompression>none</PrbCompression>
  48       <PureBases>25</PureBases>
  49       <QhgCompression>none</QhgCompression>
  50       <SeqCompression>none</SeqCompression>
  51       <Sig2Compression>gzip</Sig2Compression>
  52       <SmtFilter>failed-chastity</SmtFilter>
  53       <SmtRelation>le</SmtRelation>
  54       <SmtThreshold>1.000000</SmtThreshold>
  55     </BaseCallParameters>
  56     <Cycles First="1" Last="37" Number="37" />
  57     <Input Path="C1-37_Firecrest1.3.2_25-03-2009_diane" />
  58     <RunParameters>
  59       <AutoCycleFlag>1</AutoCycleFlag>
  60       <BasecallFlag>1</BasecallFlag>
  61       <Compression>gzip</Compression>
  62       <CompressionSuffix>.gz</CompressionSuffix>
  63       <Deblocked>0</Deblocked>
  64       <DebugFlag>0</DebugFlag>
  65       <FirstRunOnlyFlag>0</FirstRunOnlyFlag>
  66       <ImagingReads Index="1">
  67         <FirstCycle>1</FirstCycle>
  68         <LastCycle>37</LastCycle>
  69         <RunFolder>/zfs1/wold-lab/diane/sequencer/090307_HWI-EAS229_0097_30U0BAAXX</RunFolder>
  70       </ImagingReads>
  71       <Instrument>HWI-EAS229</Instrument>
  72       <IterativeMatrixFlag>0</IterativeMatrixFlag>
  73       <MakeFlag>1</MakeFlag>
  74       <MaxCycle>-1</MaxCycle>
  75       <MinCycle>-1</MinCycle>
  76       <Prb></Prb>
  77       <Reads Index="1">
  78         <FirstCycle>1</FirstCycle>
  79         <LastCycle>37</LastCycle>
  80         <RunFolder>/zfs1/wold-lab/diane/sequencer/090307_HWI-EAS229_0097_30U0BAAXX</RunFolder>
  81       </Reads>
  82       <RunFolder>/zfs1/wold-lab/diane/sequencer/090307_HWI-EAS229_0097_30U0BAAXX</RunFolder>
  83       <RunFolderDate>090307</RunFolderDate>
  84       <RunFolderId>97</RunFolderId>
  85       <SelectedFolders />
  86       <SelectedTiles />
  87       <Sig2></Sig2>
  88     </RunParameters>
  89     <Software Name="Bustard" Version="1.3.2" />
  90     <TileSelection>
  91       <Lane Index="1">
  92         <Sample>s</Sample>
  93         <TileRange Max="100" Min="1" />
  94       </Lane>
  95       <Lane Index="2">
  96         <Sample>s</Sample>
  97         <TileRange Max="100" Min="1" />
  98       </Lane>
  99       <Lane Index="3">
 100         <Sample>s</Sample>
 101         <TileRange Max="100" Min="1" />
 102       </Lane>
 103       <Lane Index="4">
 104         <Sample>s</Sample>
 105         <TileRange Max="100" Min="1" />
 106       </Lane>
 107       <Lane Index="5">
 108         <Sample>s</Sample>
 109         <TileRange Max="100" Min="1" />
 110       </Lane>
 111       <Lane Index="6">
 112         <Sample>s</Sample>
 113         <TileRange Max="100" Min="1" />
 114       </Lane>
 115       <Lane Index="7">
 116         <Sample>s</Sample>
 117         <TileRange Max="100" Min="1" />
 118       </Lane>
 119       <Lane Index="8">
 120         <Sample>s</Sample>
 121         <TileRange Max="100" Min="1" />
 122       </Lane>
 123     </TileSelection>
 124     <Time>
 125       <Start>25-03-09 15:23:10 PDT</Start>
 126     </Time>
 127     <User Name="diane" />
 128   </Run>
 129 </BaseCallAnalysis>