[Bioc-sig-seq] readAligned and BAM format

[Daniel Klevebring]

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

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