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samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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CRAM writer doesn't gzip the SAMFileHeader block in the first container #1422

Closed cmnbroad closed 4 years ago

cmnbroad commented 5 years ago

Although it is permitted by the spec to use a raw block (compressing the first container is optional, though only gzip is allowed), it really should be compressed.

cmnbroad commented 5 years ago

Fixed in refactoring branch.

cmnbroad commented 4 years ago

Fixed via https://github.com/samtools/htsjdk/pull/1440.