[BioC] Import Bam index (Rsamtools)

[Martin Morgan]

On 04/05/2012 08:36 AM, Francesco Mancuso wrote:
> Dear list,
> I have an error when I try to import a Bam file with the respective
> index using both method in Rsamtools "ScanBam()" and
> "open(BamFile())".The sorted file was created with "sortBam()" and the
> indexed with the function "indexBam()".
> For the sorting I obtain also a warning that I would like to understand.
> Is this happen because the file is too big and so it first splitted in
> more files and then merged?
>
> I am using the following code (with the relative output):
>   >  sortedFile<- sortBam("xxx.bam", "xxx_sorted", byQname=FALSE,
> maxMemory=512)
> [1] "xxx_sorted.bam"
> Warning message:
> In .local(file, destination, ...) : [bam_sort_core] merging from 2 files...

I think this warning is ok, just samtools telling you that to sort with 
the memory constraint you provided it had to split the file, but that 
these were merged in the fianl veraino.

>
>   >  indexedFile<- indexBam("xxx_sorted.bam")
>   >  bf = open(BamFile(sortedFile, indexedFile))
> Error in open.BamFile(BamFile("xxx_sorted.bam",  :
>     failed to load BAM index
>     file: xxx_sorted.bam.bai
> In addition: Warning message:
> In open.BamFile(BamFile("xxx_sorted.bam",  :
>     [bam_index_load] fail to load BAM index.

indexBam returns the (correct) path to the index. The samtools 
convention is that the index is named *without* the '.bai' extension, so 
for example in your case simply BamFile("xxx_sorted.bam") or 
BamFile("xxx_sorted.bam", sub(".bai$", "", indexedFile)).

Hope that helps and sorry for the rough edges. Martin

>   >  param<- ScanBamParam(flag=scanBamFlag(isUnmappedQuery=FALSE),
> what=c("qname", "pos", "qwidth", "rname"))
>   >  aln<- scanBam(sortedFile, index=indexedFile, param=param)
> Error in open.BamFile(BamFile(file, index), "rb") :
>     failed to load BAM index
>     file: xxx_sorted.bam.bai
> In addition: Warning message:
> In open.BamFile(BamFile(file, index), "rb") :
>     [bam_index_load] fail to load BAM index.
>
>
> Any suggestions is welcomed.
> Cheers,
> Francesco
>
>
>   >  sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C/en_US.UTF-8/C/C/C/C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Rsamtools_1.8.0     Biostrings_2.24.1   GenomicRanges_1.8.3
> IRanges_1.14.2      BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-4.1 stats4_2.15.0  tools_2.15.0   zlibbioc_1.2.0
>
>
>


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