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samtools / htslib

C library for high-throughput sequencing data formats
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CRAM lossy name compression and tag white/black list #314

Open jkbonfield opened 8 years ago

jkbonfield commented 8 years ago

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.

jkbonfield commented 8 years ago

I just spotted blacklist already exists (view -x), thanks Martin. I'll expand it.

jkbonfield commented 8 years ago

Lossy name compression is fixed by #326