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? 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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