Re: [Vcftools-help] on svn update

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That part of VCFtools (i.e. the Perl module) isn't my speciality, so I'm
hoping someone else will be able to help you.

A

On 31 December 2010 14:24, Mao Jianfeng <jia...@gm...> wrote:

> Dear Mr. Adam,
>
> Thanks for your kind help.
>
> I have posted a thread in VCFtools list, named "VCF file can not be
> read and merged after it was  compressed,Why?". I think that is not a
> difficult problem. But, I am a newbie. I need helps and directions.
>
> Note: tabix has been in my path. But, I can not merge the VCF files in
> the EXAMPLES folder.
>
> Jian-Feng
>
>
>
>
> 2010/12/31 Adam Auton <ada...@gm...>:
> > If the svn checkout worked, then you are at the latest version.
> > A
> >
> > On 31 December 2010 14:08, Mao Jianfeng <jia...@gm...> wrote:
> >>
> >> Dear Adam,
> >>
> >> Following your advice, I firstly ran "svn checkout
> >> https://vcftools.svn.sourceforge.net/svnroot/vcftools vcftools", and
> >> then "svn update". But, I still got "Skipped '.'  ".
> >>
> >> Could you please give me any direction?
> >>
> >> I expect your helps.
> >>
> >> Jian-Feng
> >>
> >>
> >>
> >> abt6-mao-mbp:tabix-0.2.3 jianfengmao$ svn checkout
> >> https://vcftools.svn.sourceforge.net/svnroot/vcftools vcftools
> >> A    vcftools/file_release
> >> A    vcftools/file_release/vcftools_0.1.1_source.tar.gz
> >> A    vcftools/file_release/VCFtools_0.1.3.1.tar.gz
> >> A    vcftools/file_release/vcftools_0.1.2_source.tar.gz
> >> A    vcftools/file_release/vcftools_0.1_source.tar.gz
> >> A    vcftools/file_release/VCFtools_0.1.3.2.tar.gz
> >> A    vcftools/file_release/VCFtools_0.1.3.tar.gz
> >> A    vcftools/file_release/vcftools_0.1.1_source_old.tar.gz
> >> A    vcftools/cpp
> >> A    vcftools/cpp/vcf_entry.cpp
> >> A    vcftools/cpp/vcftools.cpp
> >> A    vcftools/cpp/output_log.cpp
> >> A    vcftools/cpp/parameters.cpp
> >> A    vcftools/cpp/vcf_entry.h
> >> A    vcftools/cpp/vcftools.h
> >> A    vcftools/cpp/vcf_file_diff.cpp
> >> A    vcftools/cpp/vcf_file_filters.cpp
> >> A    vcftools/cpp/output_log.h
> >> A    vcftools/cpp/parameters.h
> >> A    vcftools/cpp/vcf_entry_setters.cpp
> >> A    vcftools/cpp/vcf_file.cpp
> >> A    vcftools/cpp/vcf_file.h
> >> A    vcftools/cpp/Makefile
> >> A    vcftools/cpp/vcf_entry_getters.cpp
> >> A    vcftools/cpp/vcf_file_output.cpp
> >> A    vcftools/perl
> >> A    vcftools/perl/vcf-subset
> >> A    vcftools/perl/FaSlice.pm
> >> A    vcftools/perl/query-vcf
> >> A    vcftools/perl/test.t
> >> A    vcftools/perl/vcf-concat
> >> A    vcftools/perl/vcf-annotate
> >> A    vcftools/perl/ChangeLog
> >> A    vcftools/perl/Vcf.pm
> >> A    vcftools/perl/vcf-convert
> >> A    vcftools/perl/vcf-isec
> >> A    vcftools/perl/vcf-validator
> >> A    vcftools/perl/vcf-to-tab
> >> A    vcftools/perl/compare-vcf
> >> A    vcftools/perl/vcf-sort
> >> A    vcftools/perl/fill-an-ac
> >> A    vcftools/perl/fill-aa
> >> A    vcftools/perl/vcf-shuffle-cols
> >> A    vcftools/perl/fill-rsIDs
> >> A    vcftools/perl/VcfStats.pm
> >> A    vcftools/perl/vcf-stats
> >> A    vcftools/perl/merge-vcf
> >> A    vcftools/perl/Makefile
> >> A    vcftools/website
> >> A    vcftools/website/VCF-poster.pdf
> >> A    vcftools/website/specs.html
> >> A    vcftools/website/src
> >> A    vcftools/website/src/index.inc
> >> A    vcftools/website/src/perl_module.inc
> >> A    vcftools/website/src/docs.inc
> >> A    vcftools/website/src/options.inc
> >> A    vcftools/website/src/specs.inc
> >> A    vcftools/website/src/license.inc
> >> A    vcftools/website/src/index.php
> >> A    vcftools/website/favicon.png
> >> A    vcftools/website/default.css
> >> A    vcftools/website/img
> >> A    vcftools/website/img/bgcontainer.gif
> >> A    vcftools/website/img/quote.gif
> >> A    vcftools/website/img/bgcode.gif
> >> A    vcftools/website/img/li.gif
> >> A    vcftools/website/img/search.gif
> >> A    vcftools/website/img/bg.gif
> >> A    vcftools/website/img/header.gif
> >> A    vcftools/website/img/bgul.gif
> >> A    vcftools/website/Makefile
> >> A    vcftools/website/README
> >> A    vcftools/website/favicon.ico
> >> A    vcftools/.project
> >> A    vcftools/.cproject
> >> A    vcftools/README.txt
> >> A    vcftools/Makefile
> >> A    vcftools/.settings
> >> A    vcftools/.settings/org.eclipse.ltk.core.refactoring.prefs
> >> A    vcftools/examples
> >> A    vcftools/examples/annotate.out
> >> A    vcftools/examples/subset.vcf
> >> A    vcftools/examples/shuffle-test.vcf
> >> A    vcftools/examples/annotate.txt
> >> A    vcftools/examples/cmp-test-a.vcf
> >> A    vcftools/examples/subset.indels.out
> >> A    vcftools/examples/query-test.out
> >> A    vcftools/examples/cmp-test-a-3.3.vcf
> >> A    vcftools/examples/cmp-test-b.vcf
> >> A    vcftools/examples/cmp-test-b-3.3.vcf
> >> A    vcftools/examples/subset.SNPs.out
> >> A    vcftools/examples/merge-test.vcf.out
> >> A    vcftools/examples/isec-n2-test.vcf.out
> >> A    vcftools/examples/annotate2.out
> >> A    vcftools/examples/concat-a.vcf
> >> A    vcftools/examples/invalid-4.0.vcf
> >> A    vcftools/examples/cmp-test.out
> >> A    vcftools/examples/concat-b.vcf
> >> A    vcftools/examples/annotate-test.vcf
> >> A    vcftools/examples/concat-c.vcf
> >> A    vcftools/examples/merge-test-a.vcf
> >> A    vcftools/examples/merge-test-b.vcf
> >> A    vcftools/examples/valid-4.0.vcf.stats
> >> A    vcftools/examples/merge-test-c.vcf
> >> A    vcftools/examples/valid-4.0.vcf
> >> A    vcftools/examples/concat.out
> >> A    vcftools/examples/valid-3.3.vcf
> >>  U   vcftools
> >> Checked out revision 399.
> >> abt6-mao-mbp:tabix-0.2.3 jianfengmao$ svn update
> >> Skipped '.'
> >>
> >>
> >>
> >>
> >>
> >> 2010/12/31 Adam Auton <ada...@gm...>:
> >> > Did you run the following command before using "svn update"?
> >> > svn checkout https://vcftools.svn.sourceforge.net/svnroot/vcftools
> >> > vcftools
> >> > Kind regards,
> >> > Adam
> >> >
> >> > On 31 December 2010 13:28, Mao Jianfeng <jia...@gm...>
> wrote:
> >> >>
> >> >> Dear VCFtools helpers,
> >> >>
> >> >> I am new to Unix and genomics.
> >> >>
> >> >> When I intent to update VCFtools, I got "Skipped ''."". I want to
> know
> >> >> what it is meaning.
> >> >>
> >> >> Thank you in Advance.
> >> >>
> >> >> Best.
> >> >>
> >> >> abt6-mao-mbp:tabix-0.2.3 jianfengmao$ svn update
> >> >> Skipped '.'
> >> >>
> >> >>
> >> >> --
> >> >> Jian-Feng, Mao
> >> >>
> >> >> the Institute of Botany,
> >> >> Chinese Academy of Botany,
> >> >>
> >> >>
> >> >>
> >> >>
> ------------------------------------------------------------------------------
> >> >> Learn how Oracle Real Application Clusters (RAC) One Node allows
> >> >> customers
> >> >> to consolidate database storage, standardize their database
> >> >> environment,
> >> >> and,
> >> >> should the need arise, upgrade to a full multi-node Oracle RAC
> database
> >> >> without downtime or disruption
> >> >> http://p.sf.net/sfu/oracle-sfdevnl
> >> >> _______________________________________________
> >> >> Vcftools-help mailing list
> >> >> Vcf...@li...
> >> >> https://lists.sourceforge.net/lists/listinfo/vcftools-help
> >> >
> >> >
> >> >
> >
> >
> >
> >
>
>
>
> --
> Jian-Feng, Mao
>
> the Institute of Botany,
> Chinese Academy of Botany,
>

-- 
Adam Auton
Post-Doctoral Research Scientist,
Wellcome Trust Centre for Human Genetics,
University of Oxford
Roosevelt Drive
Oxford
OX3 7BN
UK