CRAM: quality "*" is stored inefficiently.
@jkbonfield is already working on this.
Since Mar 18, 2016.
Assessment
This issue has not been assessed yet.
Description
Cramtools clears CF bit 1 (quality scores stored as an array) to omit storage of quality values in such cases. Htslib/Scramble keeps CF bit 1 set and stores an array of value 255 (the BAM approach).
It compresses well of course, but it's an unnecessary thing to do and potentially could lead to inconsistencies in behaviour as it's harder for us to spot interoperability errors than errors within our own package.
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