java.lang.IllegalStateException: A valid CRAM reference was not supplied and one cannot be acquired via the property settings reference_fasta or use_cram_ref_download

GitHub | s-andrews | 5 months ago
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    Allow CRAM to be read if reference sequences are missing.

    GitHub | 5 months ago | s-andrews
    java.lang.IllegalStateException: A valid CRAM reference was not supplied and one cannot be acquired via the property settings reference_fasta or use_cram_ref_download

    Root Cause Analysis

    1. java.lang.IllegalStateException

      A valid CRAM reference was not supplied and one cannot be acquired via the property settings reference_fasta or use_cram_ref_download

      at htsjdk.samtools.cram.ref.ReferenceSource.getDefaultCRAMReferenceSource()
    2. htsjdk.samtools.cram
      ReferenceSource.getDefaultCRAMReferenceSource
      1. htsjdk.samtools.cram.ref.ReferenceSource.getDefaultCRAMReferenceSource(ReferenceSource.java:108)
      1 frame
    3. HTS JDK
      SamReaderFactory$SamReaderFactoryImpl.open
      1. htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:301)
      2. htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:145)
      2 frames