Error in isCompatibleWithSkippedExons() for single-end read alignments w/ more than 3 junctions

[rcastelo]

Hi, single-end read alignments with more than 3 junctions in the cigar string cause the following error:

suppressPackageStartupMessages(library(GenomicAlignments))
suppressPackageStartupMessages(library(TxDb.Hsapiens.UCSC.hg38.knownGene))

txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
tx <- exonsBy(txdb, by="tx")
aln <- GAlignments("chr1", pos=42837180L, cigar="5S11M1710N21M1111N21M98N27M91N16M",
                   strand("+"), names="read1")
ovtx <- findOverlaps(GRanges(aln), tx, ignore.strand=FALSE)
ovtxenc <- encodeOverlaps(grglist(aln), tx, hits=ovtx,
                          flip.query.if.wrong.strand=FALSE)
maskskpovtx <- isCompatibleWithSkippedExons(ovtxenc) # error
Error in paste0(build_compatible_encoding_subpatterns(njunc), collapse = skipped_exons_subpatterns[njunc +  : 
  invalid 'collapse' argument

Here is my session information:

sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Madrid
tzcode source: internal

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

other attached packages:
 [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.18.0 GenomicFeatures_1.54.1                  
 [3] AnnotationDbi_1.64.1                     GenomicAlignments_1.38.0                
 [5] Rsamtools_2.18.0                         Biostrings_2.70.1                       
 [7] XVector_0.42.0                           SummarizedExperiment_1.32.0             
 [9] Biobase_2.62.0                           MatrixGenerics_1.14.0                   
[11] matrixStats_1.1.0                        GenomicRanges_1.54.1                    
[13] GenomeInfoDb_1.38.1                      IRanges_2.36.0                          
[15] S4Vectors_0.40.2                         BiocGenerics_0.48.1                     
[17] colorout_1.3-0                          

loaded via a namespace (and not attached):
 [1] KEGGREST_1.42.0         rjson_0.2.21            lattice_0.22-5          vctrs_0.6.5            
 [5] tools_4.3.2             bitops_1.0-7            generics_0.1.3          curl_5.2.0             
 [9] parallel_4.3.2          tibble_3.2.1            fansi_1.0.6             RSQLite_2.3.4          
[13] blob_1.2.4              pkgconfig_2.0.3         Matrix_1.6-4            dbplyr_2.4.0           
[17] lifecycle_1.0.4         GenomeInfoDbData_1.2.11 compiler_4.3.2          stringr_1.5.1          
[21] progress_1.2.3          codetools_0.2-19        yaml_2.3.7              RCurl_1.98-1.13        
[25] pillar_1.9.0            crayon_1.5.2            BiocParallel_1.36.0     DelayedArray_0.28.0    
[29] cachem_1.0.8            abind_1.4-5             tidyselect_1.2.0        digest_0.6.33          
[33] stringi_1.8.2           restfulr_0.0.15         dplyr_1.1.4             biomaRt_2.58.0         
[37] fastmap_1.1.1           grid_4.3.2              cli_3.6.2               SparseArray_1.2.2      
[41] magrittr_2.0.3          S4Arrays_1.2.0          XML_3.99-0.16           utf8_1.2.4             
[45] rappdirs_0.3.3          filelock_1.0.3          prettyunits_1.2.0       bit64_4.0.5            
[49] httr_1.4.7              bit_4.0.5               png_0.1-8               hms_1.1.3              
[53] memoise_2.0.1           BiocIO_1.12.0           BiocFileCache_2.10.1    rtracklayer_1.62.0     
[57] rlang_1.1.2             glue_1.6.2              DBI_1.1.3               xml2_1.3.6             
[61] R6_2.5.1                zlibbioc_1.48.0        

I've submitted a PR that fixes it.

cheers,

robert.