Hello ASpli maintainers/users!

I am currently having a problem running jCounts. Am using the latest devel version of ASpli as I was also getting the jCounts() Error in av[at] <- a[at] which was previously discussed here. Unsure what the new the error means though. Changing to " threshold = 1" does not help either.

Code I ran is below, have also attached head(gbcounts@junction.counts) if needed as well as session info.

Any guidance would be greatly appreciated.

-Dmitri

gtfFileName <- "Homo_sapiens.GRCh38.93.gtf"

genomeTxDb <- makeTxDbFromGFF(gtfFileName)
features <- binGenome( genomeTxDb )

gbcounts <- gbCounts(features=features, targets=targets,
minReadLength = 90, maxISize = 10000, libType="SE",strandMode=0)

asd <- jCounts(counts=gbcounts, features=features, minReadLength=90, libType="SE",strandMode=0)

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'sort': row names supplied are of the wrong length

> head(gbcounts@junction.counts)
                          junction            gene strand multipleHit          symbol gene_coordinates
1.11211.12010                noHit           noHit      *           -               -                -
1.11671.12010                noHit           noHit      *           -               -                -
1.11844.12010                noHit           noHit      *           -               -                -
1.12227.12613 ENSG00000223972:J001 ENSG00000223972      +           - ENSG00000223972    1:11869-14409
1.12697.13221                noHit ENSG00000223972      +           - ENSG00000223972    1:11869-14409
1.12697.13403                noHit ENSG00000223972      +           - ENSG00000223972    1:11869-14409
                                                                                                           bin_spanned
1.11211.12010                                                                ENSG00000223972:E001;ENSG00000223972:E002
1.11671.12010                                                                ENSG00000223972:E001;ENSG00000223972:E002
1.11844.12010                                                                ENSG00000223972:E001;ENSG00000223972:E002
1.12227.12613                                                                ENSG00000223972:E004;ENSG00000223972:E005
1.12697.13221                      ENSG00000223972:E005;ENSG00000223972:E006;ENSG00000223972:E007;ENSG00000223972:E008
1.12697.13403 ENSG00000223972:E005;ENSG00000223972:E006;ENSG00000223972:E007;ENSG00000223972:E008;ENSG00000223972:E009
              j_within_bin DLD1 HCT15 SW480 CACO2 HCT116 HCC2998 HT29 IS2 SW948 SKCO1
1.11211.12010            -    0     0     6     0      0       0    0   0     0     0
1.11671.12010            -    0     0     0     0      0       0    1   0     0     0
1.11844.12010            -    0     0     2     1      0       0    0   0     0     0
1.12227.12613            -    0     0     2     0      0       0    0   0     0     0
1.12697.13221            -    0     0     4     0      1       3    1   0     0     0
1.12697.13403            -    0     0     1     0      0       0    0   0     0     0

Session info below

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /stornext/System/data/apps/R/R-4.1.0/lib64/R/lib/libRblas.so
LAPACK: /stornext/System/data/apps/R/R-4.1.0/lib64/R/lib/libRlapack.so

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

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

other attached packages:
 [1] GenomicFeatures_1.45.1 GenomicRanges_1.45.0   GenomeInfoDb_1.29.3    ASpli_2.3.1           
 [5] AnnotationDbi_1.55.1   IRanges_2.27.2         S4Vectors_0.31.1       Biobase_2.53.0        
 [9] BiocGenerics_0.39.2    edgeR_3.35.0           limma_3.49.4          

loaded via a namespace (and not attached):
  [1] colorspace_2.0-2            rjson_0.2.20                ellipsis_0.3.2             
  [4] htmlTable_2.2.1             biovizBase_1.41.0           XVector_0.33.0             
  [7] base64enc_0.1-3             dichromat_2.0-0             rstudioapi_0.13            
 [10] DT_0.18                     bit64_4.0.5                 fansi_0.5.0                
 [13] xml2_1.3.2                  splines_4.1.0               cachem_1.0.6               
 [16] knitr_1.33                  Formula_1.2-4               Rsamtools_2.9.1            
 [19] cluster_2.1.2               dbplyr_2.1.1                png_0.1-7                  
 [22] BiocManager_1.30.16         compiler_4.1.0              httr_1.4.2                 
 [25] backports_1.2.1             lazyeval_0.2.2              assertthat_0.2.1           
 [28] Matrix_1.3-4                fastmap_1.1.0               htmltools_0.5.1.1          
 [31] prettyunits_1.1.1           tools_4.1.0                 igraph_1.2.6               
 [34] gtable_0.3.0                glue_1.4.2                  GenomeInfoDbData_1.2.6     
 [37] dplyr_1.0.7                 rappdirs_0.3.3              Rcpp_1.0.7                 
 [40] vctrs_0.3.8                 Biostrings_2.61.2           rtracklayer_1.53.1         
 [43] xfun_0.25                   stringr_1.4.0               lifecycle_1.0.0            
 [46] ensembldb_2.17.4            restfulr_0.0.13             XML_3.99-0.7               
 [49] zlibbioc_1.39.0             MASS_7.3-54                 scales_1.1.1               
 [52] BiocStyle_2.21.3            BSgenome_1.61.0             VariantAnnotation_1.39.0   
 [55] ProtGenerics_1.25.1         hms_1.1.0                   MatrixGenerics_1.5.3       
 [58] SummarizedExperiment_1.23.1 AnnotationFilter_1.17.1     RColorBrewer_1.1-2         
 [61] yaml_2.2.1                  curl_4.3.2                  memoise_2.0.0              
 [64] gridExtra_2.3               ggplot2_3.3.5               UpSetR_1.4.0               
 [67] rpart_4.1-15                biomaRt_2.49.4              latticeExtra_0.6-29        
 [70] stringi_1.7.3               RSQLite_2.2.7               BiocIO_1.3.0               
 [73] checkmate_2.0.0             filelock_1.0.2              BiocParallel_1.27.3        
 [76] rlang_0.4.11                pkgconfig_2.0.3             matrixStats_0.60.0         
 [79] bitops_1.0-7                evaluate_0.14               lattice_0.20-44            
 [82] purrr_0.3.4                 htmlwidgets_1.5.3           GenomicAlignments_1.29.0   
 [85] bit_4.0.4                   tidyselect_1.1.1            plyr_1.8.6                 
 [88] magrittr_2.0.1              R6_2.5.1                    generics_0.1.0             
 [91] Hmisc_4.5-0                 DelayedArray_0.19.1         DBI_1.1.1                  
 [94] pillar_1.6.2                foreign_0.8-81              nnet_7.3-16                
 [97] survival_3.2-12             KEGGREST_1.33.0             RCurl_1.98-1.4             
[100] tibble_3.1.3                crayon_1.4.1                utf8_1.2.2                 
[103] BiocFileCache_2.1.1         rmarkdown_2.10              jpeg_0.1-9                 
[106] progress_1.2.2              locfit_1.5-9.4              grid_4.1.0                 
[109] data.table_1.14.0           blob_1.2.2                  digest_0.6.27              
[112] pbmcapply_1.5.0             tidyr_1.1.3                 munsell_0.5.0              
[115] Gviz_1.37.2