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samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Changing to use SingletonList in Sam #1316

Closed lbergelson closed 5 years ago

lbergelson commented 5 years ago

Testing the newest version of htsjdk against picard fails with:

picard.analysis.CollectGcBiasMetricsTest.setupBuilder FAILED
    java.lang.UnsupportedOperationException
        at java.util.AbstractList.add(AbstractList.java:148)
        at java.util.AbstractList.add(AbstractList.java:108)
        at htsjdk.samtools.SAMFileHeader.addReadGroup(SAMFileHeader.java:192)
        at htsjdk.samtools.SAMRecordSetBuilder.setReadGroup(SAMRecordSetBuilder.java:163)
        at picard.analysis.CollectGcBiasMetricsTest.setupTest1(CollectGcBiasMetricsTest.java:407)
        at picard.analysis.CollectGcBiasMetricsTest.setupBuilder(CollectGcBiasMetricsTest.java:109)

This happens because of the change in https://github.com/samtools/htsjdk/pull/1286/ which changed ArrayList -> Collections.singletonList. 

    final List<SAMReadGroupRecord> readGroups = Collections.singletonList(readGroupRecord);