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If we fail to extend the buffer, we shouldn't extend ref_end. This avoids needing to check downstream everywhere we use ref_end to make sure it's not bigger than ref_end_alloc. Instead we'll just get short references and need to encode overhanging sequences against Ns. Credit to OSS_Fuzz Fixes oss-fuzz issue 499447432
Converting a file to CRAM with embed_ref=2 and SQ LN:0 triggers some
unusual code paths because we use a non-zero length field as an
indicator for the referencing having been populated. In this case we
convert sequence to Ns (albeit not overflowing buffers and in a secure
way).
However it's a wider issue. LN:-2 was permitted and it gets convered
to MAX_INT in bam. Plus "LN:" (no length) was accepted and treated as
zero. So instead of putting the fix in cram_io.c refs_from_header()
("if (h->hrecs->ref[i].len <= 0) ...") we disallow this globally for
all file formats.
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Note this isn't CVE worthy as the code it fixes appeared since the last release.