Hi samtools developer,
I found that the samtools *sort *help information (not the manual oneline)
is a little bit confusing for the part of specifying output format:
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
it makes people think that the output format value should be capital, but
actually after I tried and failed many times without idea of what happened,
I found that it actually should be lower-case one. (The manual online gives
the correct one).
I know it's just a small typo maybe and I should read the manual first
before use it, but this kind of help information is really kind of
confusing.
bless~
XL
On Wed, Dec 16, 2015 at 8:47 AM, John Marshall <[email protected]> wrote:
> New 1.3 versions of Samtools, BCFtools, and HTSlib have been released.
> These have numerous bug fixes, improvements, and new commands. The changes
> are too numerous to list here, but we would particularly like to draw your
> attention to these three items:
>
> * The old way of invoking the samtools sort subcommand has been superseded
> since samtools 1.0 and from this release no longer works:
>
> samtools sort [-f] [-o] in.bam out.prefix
>
> If you do use this obsolete way of specifying sort options, samtools will
> now in most cases fail and give you a hint about the new ways. If you are
> still using sort ‑f, ‑o, or out.prefix, convert to use -T PREFIX and/or -o
> FILE instead. See the manual page for details.
>
> * The samtools rmdup command has been restored to its basic
> functionality. It no longer immediately aborts, but it remains not
> recommended for most use.
>
> * When HTSlib has been built to use libcurl, most tools can now access
> remote files over HTTPS and via AWS S3 in addition to the previous HTTP,
> FTP, and iRODS. See HTSlib's INSTALL and Samtools's README for details.
>
> For further details of these and other changes in these releases, see the
> release notes for each project linked to at <
> http://www.htslib.org/download/>, or see all three together at <
> http://sourceforge.net/projects/samtools/files/samtools/1.3/>.
>
> These releases can be found at <http://www.htslib.org/>. Development and
> source code of these projects are linked from that web site and can be
> found in various Git repositories under <https://github.com/samtools>.
> Release archives are available at both GitHub and SourceForge.
>
> Installing the tools will also install manual pages for them. Once
> installed, you should be able to use "man samtools" etc at your command
> line to find details of new commands and functionality. Manual pages and
> other documentation are also available online at <
> http://www.htslib.org/doc/>.
>
> John
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
>
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>
--
bless~
XL
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