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
The merging of the sequence information is essentially a Reduce(). The rest
of the components are merged N-way.
Michael
On Mon, Jan 7, 2013 at 9:18 AM, Ryan C. Thompson wrote:
> With such a huge difference, I would wonder if the "c" method for GRanges
> objects is doing N-1 pairwise merges inste
With such a huge difference, I would wonder if the "c" method for
GRanges objects is doing N-1 pairwise merges instead of a single N-way
merge.
On Mon 07 Jan 2013 09:08:28 AM PST, Michael Lawrence wrote:
Would be interesting to do some profiling. Could be the merging of the
sequence info, or t
Would be interesting to do some profiling. Could be the merging of the
sequence info, or the rbind on the meta DataFrames (even with one column,
could be some overhead here).
Michael
On Mon, Jan 7, 2013 at 12:31 AM, Hahne, Florian
wrote:
> Hi Dario,
> the most efficient way to transform between
Hi Dario,
the most efficient way to transform between list-like structures of
GRanges objects and single GRanges is to use the GRangesList class in the
first place. Not sure how you came up with your initial list, but assuming
that blockRanges is already a GRangesList object, unlist(blockRanges) wi
