Hi there,
FWIW system.file() has the 'mustWork' arg for this. Strange name though
since the man page suggests it only tests for existence, not that the
file can actually be open for reading.
H.
On 01/07/2013 11:11 PM, Nicolas Delhomme wrote:
Just to clarify. I don't mean it needs to validate the BAM file (i.e. checking
that it's properly formatted), so using file.exists on the provided file paths
would be sufficient.
---------------------------------------------------------------
Nicolas Delhomme
Genome Biology Computational Support
European Molecular Biology Laboratory
Tel: +49 6221 387 8310
Email: nicolas.delho...@embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------
On 8 Jan 2013, at 02:47, Ryan Thompson wrote:
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" <h...@biostat.ucsf.edu> wrote:
On Mon, Jan 7, 2013 at 12:32 PM, Nicolas Delhomme <delho...@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.delho...@embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
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