Commits on Oct 16, 2024

1. Fix issue created in PR#1848 …

   We shouldn't be attempting to create embedded reference sequences for
   CRAM containers with reads mapped to chr -1 (ie unmapped).  We don't
   permit embed_ref in multi-ref mode and it's nonsensical for entirely
   unmapped data.
   
   The only real fix needed here is "c->ref_id < 0" just before
   calling cram_generate_reference(), but checking elsewhere can sidestep
   other potential issues and we have safety in checking in more than one
   place.
   
   Credit to OSS_Fuzz
   Fixes oss-fuzz issue 372547397

   

   jkbonfield committed Oct 16, 2024
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