Hi Martin,
On 8 Jan 2013, at 19:53, Martin Morgan wrote:
> On 01/07/2013 12:32 PM, Nicolas Delhomme 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 o
On 01/07/2013 12:32 PM, Nicolas Delhomme 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",
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 t
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 Suppor
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" wrote:
> On Mon, Jan 7, 2013 at 12:32 PM, Nicolas Delhomme
>
On Mon, Jan 7, 2013 at 12:32 PM, Nicolas Delhomme 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:
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 exi
