bed_cluster grouping different contigs together

[kcamnairb]

Hi, I've noticed a strange result with bed_cluster where it is somehow grouping together two contigs that are different but have similar names.

library(tidyverse)
library(valr)
tibble::tribble(
  ~chrom, ~start,   ~end,
  "contig_22", 177581, 177582,
  "contig_223",   5111,   5112,
) %>%
  bed_cluster(max_dist=10000)
## A tibble: 2 × 4
#  chrom       start    end   .id
#  <chr>       <dbl>  <dbl> <int>
#1 contig_22  177581 177582     1
#2 contig_223   5111   5112     1

But if the contig names are changed slightly bed_cluster will correctly group them as different:

tibble::tribble(
  ~chrom, ~start,   ~end,
  "contig_22", 177581, 177582,
  "contig_123",   5111,   5112,
) %>%
  bed_cluster(max_dist=10000)
## A tibble: 2 × 4
#  chrom       start    end   .id
#  <chr>       <dbl>  <dbl> <int>
#1 contig_123   5111   5112     1
#2 contig_22  177581 177582     2

[kriemo]

thanks for the bug report. This looks like an issue with our handling of the max_dist argument. I'll dig into this a bit more and get back to you when we have a fix.

library(tidyverse)
library(valr)
a <- tibble::tribble(
  ~chrom, ~start,   ~end,
  "contig_22", 177581, 177582,
  "contig_223",   5111,   5112,
) 
bed_cluster(a, max_dist=0)
#> # A tibble: 2 × 4
#>   chrom       start    end   .id
#>   <chr>       <dbl>  <dbl> <int>
#> 1 contig_22  177581 177582     1
#> 2 contig_223   5111   5112     2
bed_cluster(a, max_dist=5110)
#> # A tibble: 2 × 4
#>   chrom       start    end   .id
#>   <chr>       <dbl>  <dbl> <int>
#> 1 contig_22  177581 177582     1
#> 2 contig_223   5111   5112     2
bed_cluster(a, max_dist=5111)
#> # A tibble: 2 × 4
#>   chrom       start    end   .id
#>   <chr>       <dbl>  <dbl> <int>
#> 1 contig_22  177581 177582     1
#> 2 contig_223   5111   5112     1

^{Created on 2022-08-04 by the reprex package (v2.0.1)}

[kriemo]

This issue should be fixed now in the main branch. To install use:

# install.packages("devtools")
devtools::install_github('rnabioco/valr')

Feel free to reopen if you find the issue is not fixed. Thanks again for the bug report and your interest in valr.