[Bioc-sig-seq] readAligned and BAM format

[Sean Davis]

On Tue, Dec 8, 2009 at 5:05 PM, Pratap, Abhishek
<APratap at som.umaryland.edu> wrote:
> Hi Martin
>
> Just wondering if people outside the firewall/network without passw
> could download this package ?

You can, yes.  You'll want to use svn and follow the instructions that
Martin posted in the last email (below).

Sean

> -----Original Message-----
> From: bioc-sig-sequencing-bounces at r-project.org
> [mailto:bioc-sig-sequencing-bounces at r-project.org] On Behalf Of Martin
> Morgan
> Sent: Monday, November 02, 2009 8:58 AM
> To: Wu Wei
> Cc: bioc-sig-sequencing at r-project.org
> Subject: Re: [Bioc-sig-seq] readAligned and BAM format
>
> Hi Wave --
>
> svn co
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools
>
> R CMD INSTALL --clean Rsamtools
>
> see the script in Rsamtools/inst/script/readAligned_prototype.R
>
> e.g.,
>
>  source(system.file("script", "readAligned_prototype.R",
>                     package="Rsamtools"))
>  .readAligned_bam(<...>) # args like the other readAligned
>
> see ?scanBam for additional ideas.
>
> Martin
>
> Wu Wei wrote:
>> Hi Martin,
>>
>> I am also looking for that. Would you please also forward that
>> additional info to me.
>>
>> Thanks,
>> Wave
>>
>> On 2 Nov 2009, at 14:34, Martin Morgan wrote:
>>
>>> Joern Toedling wrote:
>>>> Hi everyone,
>>>>
>>>> has anybody by chance already written a parser for importing
>>>> alignments in
>>>> BAM/SAM format into objects of class AlignedRead? This format seems
>>>> to be
>>>> gaining more and more support, yet it is still absent from the
>>>> options in
>>>> function readAligned. If one of you already has written such a
> parsing
>>>> function and would not mind sharing it, please let me know.
>>>
>>> Hi Joern -- there is a package in the Bioc svn repository that does
>>> this; it is not yet in the devel branch, there are some limitations
> in
>>> terms of AlignedRead (e.g., AlignedRead currently supports only
> ungapped
>>> alignments, whereas BAM allows gapped). I'll forward additional info
>>> off-list.
>>>
>>> Martin
>>>>
>>>> Best regards,
>>>> Joern
>>>>
>>>> ---
>>>> Joern Toedling
>>>> Institut Curie -- U900
>>>> 26 rue d'Ulm, 75005 Paris, FRANCE
>>>> Tel. +33 (0)156246926
>>>>
>>>> _______________________________________________
>>>> Bioc-sig-sequencing mailing list
>>>> Bioc-sig-sequencing at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>
>>>
>>> --
>>> Martin Morgan
>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N.
>>> PO Box 19024 Seattle, WA 98109
>>>
>>> Location: Arnold Building M1 B861
>>> Phone: (206) 667-2793
>>>
>>> _______________________________________________
>>> Bioc-sig-sequencing mailing list
>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>>
>>
>> Wu Wei
>> Postdoctoral Fellow
>> Steinmetz Group, EMBL Heidelberg
>> Tex: +49 6221 387-8310 (8114)
>> Fax: +49 6221 387-8518
>> Email: wuwei at embl.de
>>
>>
>>
>>
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
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