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Fixes involving CRAM and header API for long references.#976

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jkbonfield wants to merge 3 commits into
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jkbonfield:long_cigar2
Open

Fixes involving CRAM and header API for long references.#976
jkbonfield wants to merge 3 commits into
samtools:developfrom
jkbonfield:long_cigar2

Create/update long reference length dictionary (`sdict`) together wit…

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