[Bioc-devel] readGAlignmentPairs with discordant strand
On 10/16/2015 09:28 AM, Michael Lawrence wrote:
I kind of wish it would return NA for things like seqnames and strand, but yes that would be very useful.
Could do this for seqnames() but I'm hesitant to do this for strand(). If you look at ?strand in BiocGenerics, ?*? is used when the exact strand of the location is unknown, or irrelevant, or when the "feature" at that location belongs to both strands. A pair with discordant strand belongs to both strands. Also there is a lot of code around that assumes strand() never returns NAs. H.
On Fri, Oct 16, 2015 at 9:15 AM, Herv? Pag?s <hpages at fredhutch.org> wrote:
Hi Michael, Martin, On 10/16/2015 06:48 AM, Michael Lawrence wrote:
It does seem like starting with the more general data structure is the better approach, but I couldn't find an easy way to move the paired subset of GAlignmentsList to GAlignmentPairs. You mention a coercion, but it's not obvious to me, unfortunately. Another approach would be a GAlignmentPairs where the unpaired reads have "missing" mates. I know GAlignments has no concept of missing, but it would get everything into a single data structure that is convenient for computing on pairs.
I could modify readGAlignmentPairs() to have the discordant and/or ambiguous pairs end up in th GAlignmentPairs. The ambiguous pairs could be marked as such thru a metadata col of the object or thru a proper slot. The seqnames() and strand() accessors will return * on discordant pairs. Does that sound reasonable? H.
On Fri, Oct 16, 2015 at 5:21 AM, Morgan, Martin < Martin.Morgan at roswellpark.org> wrote:
-----Original Message----- From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org] On Behalf Of Michael Lawrence Sent: Friday, October 16, 2015 7:41 AM To: bioc-devel at r-project.org Subject: [Bioc-devel] readGAlignmentPairs with discordant strand Now that GAlignmentPairs supports discordant strand between mates, how hard would it be to relax that restriction on readGAlignmentPairs()? Also, would be nice if getDumpedAlignments() returned those dumped by readGAlignmentPairs(). Right now, I'm reading a GAlignments (with the
extra
mcols) and calling makeGAlignmentPairs(). Not so convenient.
I'm not sure whether this is relevant to your use case but readGAlignmentsList returns a list of paired mates, and if appropriate (based on ScanBamParam) list elements with solo travelers. The paired portion of the list can be coerced to GAlignmentPairs if the additional structure of that class is required. Martin
Michael
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319
Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319