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Workaround for bug in Picard in ReadGroupProperties 

-- NPE caused when you call getRunDate on a read group without a date.
This commit is contained in:
Mark DePristo 2012-03-02 18:53:45 -05:00
parent 914c23da51
commit 69611af7d3
2 changed files with 21 additions and 12 deletions
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31
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
View File

@ -199,19 +199,28 @@ public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
final boolean hasAnyReads = info.nReadsSeen > 0;
final int readLength = info.readLength.getMedian(0);
table.set(rgID, "sample", rg.getSample());
table.set(rgID, "library", rg.getLibrary());
table.set(rgID, "platform", rg.getPlatform());
table.set(rgID, "center", rg.getSequencingCenter());
table.set(rgID, "date", dateFormatter.format(rg.getRunDate()));
table.set(rgID, "has.any.reads", hasAnyReads);
table.set(rgID, "is.paired.end", isPaired);
table.set(rgID, "n.reads.analyzed", info.nReadsSeen);
table.set(rgID, "simple.read.type", hasAnyReads ? String.format("%dx%d", isPaired ? 2 : 1, readLength) : "NA");
table.set(rgID, "median.read.length", hasAnyReads ? readLength : "NA" );
table.set(rgID, "median.insert.size", hasAnyReads && isPaired ? info.insertSize.getMedian(0) : "NA" );
setTableValue(table, rgID, "sample", rg.getSample());
setTableValue(table, rgID, "library", rg.getLibrary());
setTableValue(table, rgID, "platform", rg.getPlatform());
setTableValue(table, rgID, "center", rg.getSequencingCenter());
try {
setTableValue(table, rgID, "date", rg.getRunDate() != null ? dateFormatter.format(rg.getRunDate()) : "NA");
} catch ( NullPointerException e ) {
// TODO: remove me when bug in Picard is fixed that causes NPE when date isn't present
setTableValue(table, rgID, "date", "NA");
}
setTableValue(table, rgID, "has.any.reads", hasAnyReads);
setTableValue(table, rgID, "is.paired.end", isPaired);
setTableValue(table, rgID, "n.reads.analyzed", info.nReadsSeen);
setTableValue(table, rgID, "simple.read.type", hasAnyReads ? String.format("%dx%d", isPaired ? 2 : 1, readLength) : "NA");
setTableValue(table, rgID, "median.read.length", hasAnyReads ? readLength : "NA" );
setTableValue(table, rgID, "median.insert.size", hasAnyReads && isPaired ? info.insertSize.getMedian(0) : "NA" );
}
report.print(out);
}
private final void setTableValue(GATKReportTable table, final String rgID, final String key, final Object value) {
table.set(rgID, key, value == null ? "NA" : value);
}
}

2
public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java
View File

@ -38,7 +38,7 @@ public class ReadGroupPropertiesIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T ReadGroupProperties -R " + b37KGReference + " -I " + b37GoodBAM + " -L 20:10,000,000-11,000,000 -o %s",
1,
Arrays.asList("8e4d09665c0b65c971bd5dead24f95fe"));
Arrays.asList("6b8cce223af28cbadcfe87a3b841fc56"));
executeTest("ReadGroupProperties:", spec);
}
}