diff --git a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryXMLLoaderTest.java b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryXMLLoaderTest.java
index bd40c4d9a88a280890a780a72af8185a582b5fe8..5a6f370d3ffb2d121e2c11145841a8ba3ebcb291 100644
--- a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryXMLLoaderTest.java
+++ b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryXMLLoaderTest.java
@@ -37,18 +37,34 @@ public class IlluminaSummaryXMLLoaderTest extends AbstractFileSystemTestCase
IlluminaSummaryReportingPlugin.IlluminaSummaryXMLLoader.readSummaryXML(file);
ChipResultsSummary chipResultsSummary = summary.getChipResultsSummary();
+ LaneResultsSummary laneResultsSummary = summary.getLaneResultsSummary();
assertEquals(new Long(98792458L), chipResultsSummary.getClusterCountPF());
assertEquals(new Long(158466917L), chipResultsSummary.getClusterCountRaw());
assertEquals(new Long(3556528488L), chipResultsSummary.getYield());
- if (summary.getSoftware() == null)
+ // if not there yhen take the init value
+ assertEquals(new Double(0.0), chipResultsSummary.getDensityRatio());
+
+ assertEquals(new Long(381287L), laneResultsSummary.getRead().getLanes().get(0)
+ .getClusterCountRaw().getMean());
+ assertEquals(new Long(277736L), laneResultsSummary.getRead().getLanes().get(0)
+ .getClusterCountPF().getMean());
+ assertEquals(new Integer(1199819), laneResultsSummary.getRead().getLanes().get(0)
+ .getLaneYield());
+ assertEquals(new Double(79.37), laneResultsSummary.getRead().getLanes().get(0)
+ .getPercentUniquelyAlignedPF().getMean());
+
+ if (summary.getSoftware() == "")
{
- assertEquals(null, summary.getSoftware());
+ assertEquals("", summary.getSoftware());
} else
{
assertEquals("CASAVA-1.6.0", summary.getSoftware());
}
}
+ /**
+ *
+ */
protected static final String EXAMPLE = "<?xml version='1.0' ?>\n "
+ "<?xml-stylesheet type='text/xsl' href='Summary.xsl' ?>\n "
+ "<Summary> "
@@ -63,10 +79,122 @@ public class IlluminaSummaryXMLLoaderTest extends AbstractFileSystemTestCase
+ " <RunFolder>090916_42R0CAAXX</RunFolder> "
+ " </ChipSummary> "
+ " <Date>Tue Oct 20 18:15:43 2009</Date> "
- + " <ExpandedLaneSummary/> "
- + " <LaneParameterSummary/> "
- + " <LaneResultsSummary/> "
+ + " <ExpandedLaneSummary> "
+ + " <Read> "
+ + " <readNumber>1</readNumber> "
+ + " <Lane> "
+ + " <laneNumber>1</laneNumber> "
+ + " <clusterCountRaw> "
+ + " <mean>381286.80</mean> "
+ + " <stdev>28613.35</stdev> "
+ + " <sumsq>98246880000.00</sumsq> "
+ + " </clusterCountRaw> "
+ + " <errorPF> "
+ + " <mean>0.72</mean> "
+ + " <stdev>0.49</stdev> "
+ + " <sumsq>90.37</sumsq> "
+ + " </errorPF> "
+ + " <errorRaw> "
+ + " <mean>0.83</mean> "
+ + " <stdev>0.48</stdev> "
+ + " <sumsq>110.63</sumsq> "
+ + " </errorRaw> "
+ + " <infoContentPF> "
+ + " <mean>213494</mean> "
+ + " <stdev>9929</stdev> "
+ + " <sumsq>5481321756576</sumsq> "
+ + " </infoContentPF> "
+ + " <infoContentRaw> "
+ + " <mean>229532</mean> "
+ + " <stdev>11786</stdev> "
+ + " <sumsq>6338734406410</sumsq> "
+ + " </infoContentRaw> "
+ + " <percentClustersPF> "
+ + " <mean>73.03</mean> "
+ + " <stdev>2.72</stdev> "
+ + " <sumsq>890.49</sumsq> "
+ + " </percentClustersPF> "
+ + " <percentUniquelyAlignedPF> "
+ + " <mean>79.37</mean> "
+ + " <stdev>0.86</stdev> "
+ + " <sumsq>755955.73</sumsq> "
+ + " </percentUniquelyAlignedPF> "
+ + " <phasingApplied>0.8203</phasingApplied> "
+ + " <prephasingApplied>0.3881</prephasingApplied> "
+ + " <signalAverage1to3> "
+ + " <mean>526.07</mean> "
+ + " <stdev>43.17</stdev> "
+ + " <sumsq>223675.10</sumsq> "
+ + " </signalAverage1to3> "
+ + " <signalAverage2to4> "
+ + " <mean>519.91</mean> "
+ + " <stdev>41.72</stdev> "
+ + " <sumsq>208871.60</sumsq> "
+ + " </signalAverage2to4> "
+ + " <signalLoss10to20> "
+ + " <mean>1.01</mean> "
+ + " <stdev>0.40</stdev> "
+ + " <sumsq>19.25</sumsq> "
+ + " </signalLoss10to20> "
+ + " <signalLoss2to10> "
+ + " <mean>0.45</mean> "
+ + " <stdev>0.53</stdev> "
+ + " <sumsq>33.94</sumsq> "
+ + " </signalLoss2to10> "
+ + " </Lane> "
+ + " </Read> "
+ + " </ExpandedLaneSummary> "
+ + " <LaneParameterSummary/> "
+ + " <LaneResultsSummary> "
+ + " <Read> "
+ + " <readNumber>1</readNumber> "
+ + " <Lane> "
+ + " <laneNumber>1</laneNumber> "
+ + " <averageAlignScorePF> "
+ + " <mean>94.25</mean> "
+ + " <stdev>3.64</stdev> "
+ + " <sumsq>1067460.47</sumsq> "
+ + " </averageAlignScorePF> "
+ + " <clusterCountPF> "
+ + " <mean>277736</mean> "
+ + " <stdev>11981</stdev> "
+ + " <sumsq>17224950000</sumsq> "
+ + " </clusterCountPF> "
+ + " <clusterCountRaw> "
+ + " <mean>381287</mean> "
+ + " <stdev>28613</stdev> "
+ + " <sumsq>98246880000</sumsq> "
+ + " </clusterCountRaw> "
+ + "<errorPF> "
+ + "<mean>0.72</mean> "
+ + "<stdev>0.49</stdev> "
+ + "<sumsq>90.37</sumsq> "
+ + "</errorPF> "
+ + "<laneYield>1199819</laneYield> "
+ + "<oneSig> "
+ + "<mean>536</mean> "
+ + "<stdev>46</stdev> "
+ + "<sumsq>256164</sumsq> "
+ + "</oneSig> "
+ + "<percentClustersPF> "
+ + "<mean>73.03</mean> "
+ + "<stdev>2.72</stdev> "
+ + "<sumsq>890.49</sumsq> "
+ + "</percentClustersPF> "
+ + "<percentUniquelyAlignedPF> "
+ + "<mean>79.37</mean> "
+ + "<stdev>0.86</stdev> "
+ + "<sumsq>755955.73</sumsq> "
+ + "</percentUniquelyAlignedPF> "
+ + "<signal20AsPctOf1> "
+ + "<mean>82.19</mean> "
+ + "<stdev>5.09</stdev> "
+ + "<sumsq>3103.16</sumsq> "
+ + "</signal20AsPctOf1> "
+ + " </Lane> "
+ + " </Read> "
+ + " </LaneResultsSummary> "
+ " <TileErrorsByLane/> "
- // + " <Software>CASAVA-1.6.0</Software> "
+ + " <Software>CASAVA-1.6.0</Software> "
+ "</Summary>";
}