Hello, Is it possible to use methods such as scanBamHeader on a BAM file that is described by an URL ? I only notice it taking file path arguments. I have the BAM file and its .bai file in a directory on a web server. -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia

On 01/10/2012 09:00 PM, Dario Strbenac wrote: > Hello, > > Is it possible to use methods such as scanBamHeader on a BAM file > that is described by an URL ? I only notice it taking file path > arguments. I have the BAM file and its .bai file in a directory on a > web server. Hi Dario -- Yes this should work, just provide the url as a character(1), fl = "http://..." ## or ftp if that's what the server serves scanBamHeader(fl) The vignette illustrates this. Martin > > -------------------------------------- Dario Strbenac Research > Assistant Cancer Epigenetics Garvan Institute of Medical Research > Darlinghurst NSW 2010 Australia > > _______________________________________________ Bioconductor mailing > list Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

>just provide the url as a character(1), Ah, I tried this and it didn't work at first. But I've narrowed it down to a network issue here. There was a brief period of time it was working, so I know it will work at a later time.