On Tue, Dec 8, 2009 at 5:05 PM, Pratap, Abhishek <[email protected]> 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: [email protected] > [mailto:[email protected]] On Behalf Of Martin > Morgan > Sent: Monday, November 02, 2009 8:58 AM > 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 > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
