[Bioc-devel] BamFile validation

Couldn't one test for existence by trying to open the BamFile object, and possibly read one sequence (or maybe just read the header since I guess a valid bam file can contain zero sequences)?

On Jan 7, 2013 1:32 PM, "Henrik Bengtsson" <hb at biostat.ucsf.edu> wrote:
On Mon, Jan 7, 2013 at 12:32 PM, Nicolas Delhomme <delhomme at embl.de> wrote:

Hi Martin, Marc,

I'm now implementing the use of BamFile objects in easyRNASeq and I like them. I think it would be very useful if when constructing a BamFile the existence of the path and index could be tested; i.e. this works: BamFile("test.bam","test.bam.bai") although these files do not exist. Is there a reason that this validation is not done? If there is, could a validation parameter be added (set to FALSE by default to keep the current behavior) that would check for the files' existence?

Good idea - I propose argument 'mustExist'.

My $0.02

/Henrik

The same goes for the yieldSize argument, i.e. this works BamFile("test.bam","test.bam.bai",yieldSize=-1), although I'm not sure what a -1 yieldSize means. I can of course do these validations within easyRNASeq, but anyone else building packages on top of BamFile would probably want to do the same...


A related point unclear at the moment in the documentation is what the index filename should be: i.e. scanBam expects as the index the same value as for the bam filename (that assumes the user has not renamed his bam.bai file  and you never know what users might be doing... :-S ... ) but the BamFile Rd page says:

file: A character vector of BAM file paths
index:  A character vector of indices (forBamFile);

so it's unclear to me what the index character vector should contain.

Thanks again for this set of class, they're really handy!

Here's my sessionInfo:

R Under development (unstable) (2012-10-02 r60861)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] Rsamtools_1.11.14     Biostrings_2.27.8     GenomicRanges_1.11.21
[4] IRanges_1.17.24       BiocGenerics_0.5.6    BiocInstaller_1.9.6

loaded via a namespace (and not attached):
[1] bitops_1.0-5   stats4_2.16.0  tools_2.16.0   zlibbioc_1.5.0

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany