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: [email protected] [[email protected]] On Behalf Of Martin Morgan [[email protected]] Sent: 02 November 2009 14:58 To: Wu Wei Cc: [email protected] 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 >>> [email protected] >>> 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 >> [email protected] >> 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: [email protected] > > > > -- 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 [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
