[Bioc-sig-seq] readAligned and BAM format

[Martin Morgan]

Hi Daniel --

Remember that Rsamtools is not even in the devel repository; it is a
moving target. The error below requires an update, perhaps from svn, of
Rsamtools dependencies, specifically IRanges.

Use the development version of R with these packages.

Martin

Daniel Klevebring wrote:
> Hi all, 
> 
> Rsamtools looks very interesting. I tried installing it as described below but I get
> 
> gcc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include  -I/sw/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Resources/library/IRanges/include"  -D_USE_KNETFILE -Dinline="" -D_FILE_OFFSET_BITS=64 -fPIC  -g -O2 -c cigar.c -o cigar.o
> cigar.c: In function ‘cigar_to_list_of_IRanges’:
> cigar.c:257: error: ‘RangeAEAE’ undeclared (first use in this function)
> cigar.c:257: error: (Each undeclared identifier is reported only once
> cigar.c:257: error: for each function it appears in.)
> cigar.c:257: error: expected ‘;’ before ‘range_aeae’
> cigar.c:262: error: ‘range_aeae’ undeclared (first use in this function)
> cigar.c:262: warning: implicit declaration of function ‘new_RangeAEAE’
> cigar.c:279: warning: implicit declaration of function ‘RangeAEAE_asLIST’
> cigar.c:279: warning: assignment makes pointer from integer without a cast
> make: *** [cigar.o] Error 1
> ERROR: compilation failed for package ‘Rsamtools’
> * Removing ‘/Library/Frameworks/R.framework/Resources/library/Rsamtools’
> 
> I'm on Mac OS X 10.6.1 with R 2.9.2 and Rsamtools 0.1.16. Any ideas on this? 
> 
> Thanks
> Daniel Klevebring
> 
> ________________________________________
> From: bioc-sig-sequencing-bounces at r-project.org [bioc-sig-sequencing-bounces at r-project.org] On Behalf Of Martin Morgan [mtmorgan at fhcrc.org]
> Sent: 02 November 2009 14:58
> 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


-- 
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