Add documentation on CRAM compression profiles. #1659
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jmarshall
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May 26, 2022
doc/samtools.1
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| @@ -937,18 +937,56 @@ block compression. | |||
| CRAM output only; defaults to 0 (off). Permits use of lzma in CRAM | |||
| block compression. | |||
| .TP | |||
| .BI use_fqz= 0|1 | |||
| CRAM >= 3.1 output only; enables and disables the fqzcomp quality | |||
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These could be pretty-printed as ≥, which makes a difference to the HTML view on http://htslib.org/doc and also in man samtools if your terminal is in an UTF-8 locale (which it probably is, these days):
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| CRAM >= 3.1 output only; enables and disables the fqzcomp quality | |
| CRAM \(>= 3.1 output only; enables and disables the fqzcomp quality |
(There are existing examples in the --subsample paragraph of the view man page.)
Also document the newer options that appeared with CRAM 3.1 and above. Fixes samtools#1656
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Also document the newer options that appeared with CRAM 3.1 and above.
Fixes #1656