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CRAM lossy name compression and tag white/black list #314

@jkbonfield

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@jkbonfield

Experimental lossy name compression has appeared in the latest Scramble. After more evaluation and testing this needs porting to samtools and giving appropriate API hooks for enabling / disabling it.

We also need --include-tags and --exclude-tags (or --tag-whitelist and --tag-blacklist) options for samtools view so that we can filter-in/out specific auxiliary tags.

Finally also consider adding https://github.com/jkbonfield/qual_loss/ as a samtools command, once completed.

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