Hello,

Is there a more straightforward way of generating a GRanges o GRangesList object with the cigar ranges of genomic alignments in reference space?. I am using cigarRangesAlongReferenceSpace, but it returns an IRangesList. Would it make sense that cigarRangesAlongReferenceSpace return a GRangesList instead (because it is in reference space)? For example, junctions return a GRangesList object.

So far, what I am doing is convert the IRangesList to a GRangesList, but it is not straightforward. Is there another way?

Thanks

  library(GenomicAlignments)

# Dummy GAlignments
  gal <- GAlignments(
    seqnames=c('chr1','chr2'),
    pos=c(1000,2000),
    cigar = c('30M2000N12M','15M40N10M')
  )
  gal

GAlignments object with 2 alignments and 0 metadata columns:
      seqnames strand       cigar    qwidth     start       end     width     njunc
         <Rle>  <Rle> <character> <integer> <integer> <integer> <integer> <integer>
  [1]     chr1      * 30M2000N12M        42      1000      3041      2042         1
  [2]     chr2      *   15M40N10M        25      2000      2064        65         1
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths


# Extract the matches
  cirs <- cigarRangesAlongReferenceSpace(cigar(gal),pos = start(gal),ops = 'M',drop.empty.ranges = T)
  cirs

IRangesList object of length 2:
[[1]]
IRanges object with 2 ranges and 0 metadata columns:
          start       end     width
      <integer> <integer> <integer>
  [1]      1000      1029        30
  [2]      3030      3041        12

[[2]]
IRanges object with 2 ranges and 0 metadata columns:
          start       end     width
      <integer> <integer> <integer>
  [1]      2000      2014        15
  [2]      2055      2064        10

# Convert to GRanges
  ske <- cirs@partitioning # Or PartitioningByEnd(cirs)
  lens <- lengths(cirs)
  cgrs <- GRanges(
    seqnames=rep(seqnames(gal),lens),
    ranges=unlist(cirs),
    strand=rep(strand(gal),lens),
    mcols(gal)[rep(1:length(gal),lens),,drop=F])
  cgrs <- relist(cgrs,ske)
  cgrs

GRangesList object of length 2:
[[1]]
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1 1000-1029      *
  [2]     chr1 3030-3041      *
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths

[[2]]
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr2 2000-2014      *
  [2]     chr2 2055-2064      *
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths

sessionInfo( )

R version 4.4.3 (2025-02-28)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.21.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Madrid
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GenomicAlignments_1.40.0    Rsamtools_2.20.0            Biostrings_2.72.0           XVector_0.44.0             
 [5] SummarizedExperiment_1.34.0 Biobase_2.64.0              MatrixGenerics_1.16.0       matrixStats_1.3.0          
 [9] GenomicRanges_1.56.0        GenomeInfoDb_1.40.1         IRanges_2.38.0              S4Vectors_0.42.0           
[13] BiocGenerics_0.50.0        

loaded via a namespace (and not attached):
 [1] crayon_1.5.2            httr_1.4.7              UCSC.utils_1.0.0        jsonlite_1.8.8          DelayedArray_0.30.1    
 [6] grid_4.4.3              abind_1.4-5             bitops_1.0-7            compiler_4.4.3          codetools_0.2-20       
[11] BiocParallel_1.38.0     rstudioapi_0.16.0       lattice_0.22-6          R6_2.5.1                SparseArray_1.4.8      
[16] parallel_4.4.3          GenomeInfoDbData_1.2.12 Matrix_1.7-0            tools_4.4.3             zlibbioc_1.50.0        
[21] S4Arrays_1.4.1

> as(gal, "GRangesList")
GRangesList object of length 2:
[[1]]
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1 1000-1029      *
  [2]     chr1 3030-3041      *
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths

[[2]]
GRanges object with 2 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr2 2000-2014      *
  [2]     chr2 2055-2064      *
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths

This coercion uses cigarRangesAlongReferenceSpace() behind the scene.

You rarely need to use cigarRangesAlongReferenceSpace() or any of the other low-level utilities documented in ?'cigar-utils' _directly_. These are the low-level workhorses behind higher level functionalities like as(<GAlignments>, "GRangesList"), as(<GAlignments>, "GRanges"), grglist(<GAlignments>), rglist(<GAlignments>), granges(<GAlignments>), ranges(<GAlignments>), etc...