Sounds very sensible not to double count in the context of tallying
variants. I was more concerned with reducing which as the default
behavior for scanBam and other functions.
I wanted to bring up the samtools behavior as - for me at least -
inconsistencies between Rsamtools and samtools have been
Hi Thomas, Michael,
makeVRangesFromGRanges has been added to 1.13.34. The
methods-VRanges-class.R file was already large so I added
makeVRangesFromGRanges.R.
A few notes:
- '...' was replaced with 'keep.extra.columns'
- row names are propagated automatically so I removed the explicit
row.n
Maybe Rsamtools would want to follow this precedent. I think there might be
a difference between fishing out alignments from a SAM/BAM, and deriving a
summary (tallyVariants) from a BAM. It seems like an argument could be made
for a tally set to not contain duplicates.
On Mon, Feb 23, 2015 at 11:0
On 02/23/2015 11:05 AM, Leonard Goldstein wrote:
Hi Michael and Thomas,
I ran into the same problem in the past (i.e. when I started working
with functions like scanBam I expected them not to return the same
alignment multiple times)
One thing to consider might be that returning alignments mult
Hi Michael and Thomas,
I ran into the same problem in the past (i.e. when I started working
with functions like scanBam I expected them not to return the same
alignment multiple times)
One thing to consider might be that returning alignments multiple
times is consistent with the behavior of the s
Hi,
It took me a while, but I was confused by getting different results
when using 'which' in reading BAM files. In my use case, I have a
GRanges with 15 ranges (different exons from the transcripts of a
gene) and I get much higher coverage values than simply using the
range of the 15 ranges.
I n
Hi,
From v2, baySeq has moved from storing data in matrices to arrays, to
allow for multi-dimensional analyses. This looks like an unintended
consequence of that change - I'll look into it and see if it's fixable,
or whether it's indices only from now on.
Thanks for bringing it to my attentio
