[BUG] Character List columns cause an error in join_overlap_left()

[smped]

Hi Stuart,

Hope things are going well & I'm still finding this to be such a useful package.

I've come across a problem with join_overlap_left() if the right ranges contain a CharacterList column, as might be output from reduce_ranges() depending on the function being used. If there is a CharacterList column, the fuction simply outputs the error:

Error: subscript contains NAs

As a minimal reproducible example:

library(plyranges)
x <- GRanges(c("chr1:1-10", "chr1:21-30")) 
y <- GRanges("chr1:25-30") %>% mutate(letter = CharacterList("a"))
join_overlap_left(x, y)
Error: subscript contains NAs

This produces the above error, however, the same error doesn't occur when using a generic S3 list column

y$letter <- as(y$letter, "list") 
join_overlap_left(x, y)

GRanges object with 2 ranges and 1 metadata column:
      seqnames    ranges strand | letter
         <Rle> <IRanges>  <Rle> | <list>
  [1]     chr1      1-10      * |       
  [2]     chr1     21-30      * |      a
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

I also noticed that I couldn't find a way to change the original CharacterList column into an S3 list using mutate(), but that might be a side issue.

y <- GRanges("chr1:25-30") %>% mutate(letter = CharacterList("a"))
mutate(y, letter = as(letter, "list"))

GRanges object with 1 range and 1 metadata column:
      seqnames    ranges strand |      letter
         <Rle> <IRanges>  <Rle> | <character>
  [1]     chr1     25-30      * |           a
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

This shouldn't (to my mind) produce a character column, but should return a list column. If the object is more complicated than my toy example, it can cause the data to fall apart pretty badly.

y <- GRanges(c("chr1:25-30", "chr1:101")) %>% 
  mutate(letter = CharacterList(list("a", c("b", "c")))) 
y %>%
  mutate(letter = as(letter, "list"))

GRanges object with 2 ranges and 1 metadata column:
      seqnames    ranges strand |      letter
         <Rle> <IRanges>  <Rle> | <character>
  [1]     chr1     25-30      * |           a
  [2]     chr1       101      * |           a
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
Warning message:
In recycleSingleBracketReplacementValue(value, x, nsbs) :
  number of values supplied is not a sub-multiple of the number of values to be replaced

Hopefully that's not too much information.

Cheers,

Steve

R session information

─ Session info ──────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.1.0 (2021-05-18)
 os       Ubuntu 20.04.2 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  C.UTF-8                     
 ctype    C.UTF-8                     
 tz       Australia/Adelaide          
 date     2021-07-02                  

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[smped]

I should also add that I tracked it down to the following line from .join_overlap_left()

mcols_outer <- na_dframe(mcols(right), sum(only_left))

Might save you a few minutes while debugging

[sa-lee]

Thanks for the report Steve, I'll try to get to this one on the weekend :)

[hw538]

the same bug happened when the meta col is 'DNAStringSet' , would you mind adding support to this? Thank you ~