On 11 Sep 2014, at 03:00, Dario Strbenac <[email protected]> wrote:
> -l INT Set compression level, from 0 to 9 [-1]
>
> If valid values range from 0 to 9, why is the default -1 ? Also, do higher
> values correspond to more compression ? The documentation is not explicit as
> to how the numbers relate to the amount of compression.
The compression level setting works the same way as in zlib and the gzip
command: 0 is uncompressed, 1 is fast but minimal compression, and 9 is the
best compression but likely slower (at least for compressing/writing).
-1 is an internal detail meaning the format's default compression setting; e.g.
for BAM it is zlib's default setting, namely 6. But there's no need to
obfuscate the help message with that, and the documentation should indeed
describe the levels; so I've updated the manual accordingly [1].
John
[1]
https://github.com/samtools/samtools/commit/ef00bd8688673c4e0d87f31903cfe8e19cd8fbeb
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