[BioC] BAM files to Genomic Ranges object

[Martin Morgan]

On 01/09/2013 06:08 AM, jluis.lavin at unavarra.es wrote:
> Hello everybody,
>
> I've been told about a very nice R package called Repitools. It has many
> interesting features but the use of some of them remains a little unclear
> to me yet.
> There are some subjects about this tool I'll have to ask about, in this
> list, but first of all I need to convert some BAM files into GRanges
> objects.
> To do so I read about BAM2GenomicRanges function. Reading the package
> documentation, I tried to convert 3 BAM files into GRanges. I used the
> following instructions:
>
> *(where "/path/to/ANALYSIS/folder/" is the directory where my BAM files are)
>
> bgr <- BAM2GRanges('/path/to/ANALYSIS/folder/',

Hi -- I'm not a regular user of BAM2GRanges, but I think the first argument is 
supposed to be the path to the bam file, not to the directory in which the bam 
file is located.

After

 > example(BAM2GRanges)

compare

 > BAM2GRanges(tiny.BAM)

with

 > BAM2GRanges(dirname(tiny.BAM))

Martin

> what = c("rname", "strand", "pos", "qwidth"),
> flag = scanBamFlag(isUnmappedQuery = FALSE, isDuplicate = FALSE),
> verbose = TRUE)
>
> And I get this error message:
>
> Reading BAM file AW-07.
> [bam_header_read] bgzf_check_EOF: Invalid argument
> [bam_header_read] invalid BAM binary header (this is not a BAM file).
> Error in open.BamFile(BamFile(file, index), "rb") :
>    SAM/BAM header missing or empty
>    file: '/path/to/ANALYSIS/folder/'
>
> The BAM files I'm using here where produced by a tophat alignment and used
> in R previously for other analysis with this R code:
>
> library(Rsamtools)
> library(GenomicFeatures)
>
> bamlist=list()
> src_files=list.files(pattern="*.bam")
>
> for(filename in src_files)
> {
> 	tmp=readBamGappedAlignments(filename)
> 	bamlist[[length(bamlist)+1]]=GRanges(seqnames=rname(tmp),
> 	ranges=IRanges(start=start(tmp),end=end(tmp)),
> 	strand=rep("*",length(tmp)))
> }
>
>
> names(bamlist)=src_files
>
> My question is, Why are now considered as invalid BAM files when they
> previously worked as correct BAM files? Am I mistaken about the meaning of
> the error message?Did I miss something in the code?
>
> Thanks in advance for your kind help.
>
> JL
>
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