Am I misunderstanding the usage of first() and second() from the GAlignmentPairs. My understanding is that it should return the first and second mates for each pairs, right? I think it's pretty recent as I have used it before. Also, I'm seeing this with other bam files.

Many thanks

aln <- readGAlignmentPairs("https://dovetail-public.s3-us-west-2.amazonaws.com/TPC-29-37.bam")

length(aln)
# [1] 3164606

length(second(aln))
# [1] 3164606

length(first(aln))
# [1] 2

sessionInfo( )

 R version 4.0.3 (2020-10-10)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Ubuntu 18.04.5 LTS

 Matrix products: default
 BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

 other attached packages:
  [1] coolR_0.0.0.9000            rhdf5_2.32.4
  [3] InteractionSet_1.16.0       tidyr_1.1.2
  [5] dplyr_1.0.2                 ggplot2_3.3.2
  [7] rtracklayer_1.48.0          GenomicAlignments_1.24.0
  [9] Rsamtools_2.4.0             Biostrings_2.56.0
 [11] XVector_0.28.0              SummarizedExperiment_1.18.2
 [13] DelayedArray_0.14.1         matrixStats_0.57.0
 [15] Biobase_2.48.0              GenomicRanges_1.40.0
 [17] GenomeInfoDb_1.24.2         IRanges_2.22.2
 [19] S4Vectors_0.26.1            BiocGenerics_0.34.0

 loaded via a namespace (and not attached):
  [1] Rcpp_1.0.5             compiler_4.0.3         pillar_1.4.6
  [4] bitops_1.0-6           tools_4.0.3            zlibbioc_1.34.0
  [7] lifecycle_0.2.0        tibble_3.0.3           gtable_0.3.0
 [10] lattice_0.20-41        pkgconfig_2.0.3        rlang_0.4.7
 [13] Matrix_1.2-18          GenomeInfoDbData_1.2.3 withr_2.3.0
 [16] generics_0.0.2         vctrs_0.3.4            tidyselect_1.1.0
 [19] grid_4.0.3             glue_1.4.2             R6_2.4.1
 [22] XML_3.99-0.5           BiocParallel_1.22.0    Rhdf5lib_1.10.1
 [25] purrr_0.3.4            magrittr_1.5           scales_1.1.1
 [28] ellipsis_0.3.1         colorspace_1.4-1       RCurl_1.98-1.2
 [31] munsell_0.5.0          crayon_1.3.4

From ?readGAlignmentPairs

> bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
                            mustWork=TRUE)
bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",
+                             mustWork=TRUE)
> galp1 <- readGAlignmentPairs(bamfile)
> length(galp1)
[1] 1572
> length(first(galp1))
[1] 1572
> length(second(galp1))
[1] 1572

You should probably check your install though, using

library(BiocManager)
valid()

That's an old version of GenomicAlignments for your version of R.

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] GenomicAlignments_1.26.0    Rsamtools_2.6.0            
 [3] Biostrings_2.58.0           XVector_0.30.0             
 [5] SummarizedExperiment_1.20.0 Biobase_2.50.0             
 [7] MatrixGenerics_1.2.0        matrixStats_0.57.0         
 [9] GenomicRanges_1.42.0        GenomeInfoDb_1.26.1        
[11] IRanges_2.24.0              S4Vectors_0.28.0           
[13] BiocGenerics_0.36.0        

loaded via a namespace (and not attached):
 [1] lattice_0.20-41        crayon_1.3.4           bitops_1.0-6          
 [4] grid_4.0.0             zlibbioc_1.36.0        Matrix_1.2-18         
 [7] BiocParallel_1.24.1    tools_4.0.0            RCurl_1.98-1.2        
[10] DelayedArray_0.16.0    compiler_4.0.0         GenomeInfoDbData_1.2.4

Thanks James, didn't realize I was out of sync with the current BioC version. Didn't fix the issue though.

Thanks Martin, as usual you nailed it. This is a good reminder that I should have pasted a full working example, not lines of code from an already running session. Again, dplyr is throwing me a curve ball... As much as I like some of dplyr functionality, I think that it's behavior is unacceptable... The package should not try to work on any objects it get thrown... been happening way to frequently, anyhow, here is a full working example showing the issue:

library(GenomicAlignments)

aln <- readGAlignmentPairs("https://dovetail-public.s3-us-west-2.amazonaws.com/TPC-29-37.bam")

length(aln)
## [1] 3164606                                                                                                                                                                                            

length(first(aln))
## [1] 3164606                                                                                                                                                                                            

library(dplyr)

length(first(aln))
## [1] 2                                                                                                                                                                                                  

length(GenomicAlignments::first(aln))
## [1] 3164606

Thanks again. my solution from now is to NOT load dplyr on the stack and start using fully referenced method (ie dplyr::first())

Marco

 sessionInfo()
 R version 4.0.3 (2020-10-10)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Ubuntu 18.04.5 LTS

 Matrix products: default
 BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

 other attached packages:
  [1] dplyr_1.0.2                 GenomicAlignments_1.24.0
  [3] Rsamtools_2.4.0             Biostrings_2.56.0
  [5] XVector_0.28.0              SummarizedExperiment_1.18.2
  [7] DelayedArray_0.14.1         matrixStats_0.57.0
  [9] Biobase_2.48.0              GenomicRanges_1.40.0
 [11] GenomeInfoDb_1.24.2         IRanges_2.22.2
 [13] S4Vectors_0.26.1            BiocGenerics_0.34.0

 loaded via a namespace (and not attached):
  [1] magrittr_2.0.1         zlibbioc_1.34.0        tidyselect_1.1.0
  [4] BiocParallel_1.22.0    lattice_0.20-41        R6_2.5.0
  [7] rlang_0.4.9            tools_4.0.3            grid_4.0.3
 [10] ellipsis_0.3.1         tibble_3.0.4           lifecycle_0.2.0
 [13] crayon_1.3.4           Matrix_1.2-18          GenomeInfoDbData_1.2.3
 [16] purrr_0.3.4            vctrs_0.3.5            bitops_1.0-6
 [19] RCurl_1.98-1.2         glue_1.4.2             pillar_1.4.7
 [22] compiler_4.0.3         generics_0.1.0         pkgconfig_2.0.3