plyranges
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tidyomics
`read_bam()` return value
Current read_bam() returns a GAlignments or GAlignmentsList. I think we want to hide that data structure from the user. It could instead return a GRanges (GroupedGRanges for a GAlignmentsList) with fields from the GAlignments as metadata columns. There then needs to be a way to do the equivalent of grglist(ga), i.e., chop the ranges (into a GroupedGRanges) by introns or any gap. Maybe chop_by_introns() and chop_by_gaps() (both N's and D's).
For paired end data, is there an easy way to extract the first and second ends as GRanges? It looks like the user gets a GAlignmentsList (I guess eventually a GroupedGRanges), so there would need to be an obvious way of getting the first (or second) member of each group. I guess after the user has already explicitly dropped the unpaired reads (singleton groups).
I think in the original API spec there was a split_alignments function, which I haven’t got around to implementing yet.
From: Michael Lawrence [email protected]
Sent: Monday, 4 December 2017 4:27:21 AM
To: sa-lee/plyranges
Cc: Subscribed
Subject: Re: [sa-lee/plyranges] read_bam() return value (#15)
For paired end data, is there an easy way to extract the first and second ends as GRanges? It looks like the user gets a GAlignmentsList (I guess eventually a GroupedGRanges), so there would need to be an obvious way of getting the first (or second) member of each group. I guess after the user has already explicitly dropped the unpaired reads (singleton groups).
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Yea, but I was thinking chop_ might be a better verb. Just because "split" already has a meaning in R. And mentioning introns makes the meaning more obvious.
@lawremi i've implmented chop in https://github.com/sa-lee/plyranges/blob/operators-class/R/ranges-chop.R is that what you meant?
No, what I mean is the behaivor of calling grglist() on a GAlignments, except instead of returning a GRangesList, we return a grouped GRanges. This is going to break ranges up into smaller pieces, leaving out the introns and optionally deletions.