I'm having an issue importing (part of) a BAM file into R using the Rsamtools readGAlignmentPairs() function. In particular, I raise a peculiar error ("subscript contains NAs") when using a ScanBamParam object with bamMapqFilter set to not NA and > 0.  This only happens with some BAM files, so it may be a problem with the particular BAM file and not the Rsamtools code. I apologize for any mistakes, this is my first post. Any help with the following issue would be greatly appreciated. For example:

gr <- GRanges('chr1',IRanges(1e6,2e6))
sbp <- ScanBamParam(mapqFilter=NA,which=gr)
ga <- readGAlignmentPairs(bamFile,param=sbp)

works without issue. However,

gr <- GRanges('chr1',IRanges(1e6,2e6))
sbp <- ScanBamParam(mapqFilter=10,which=gr)
ga <- readGAlignmentPairs(bamFile,param=sbp)
Error: subscript contains NAs

produces the error. Inspection suggests there are about 10000 reads in this region that have mapq > 10, so I'm not sure why an error is being raised. Here is the traceback()

14: stop(wmsg(...), call. = FALSE)
13: .subscript_error("subscript contains NAs")
12: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, 
        allow.NAs = allow.NAs)
11: NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, 
        allow.NAs = allow.NAs)
10: normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE)
9: extractROWS(x, i)
8: extractROWS(x, i)
7: gal[idx2]
6: gal[idx2]
5: .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode, 
       use.mcols = use.mcols)
4: readGAlignmentPairs(bam, character(0), use.names = use.names, 
       param = param, with.which_label = with.which_label, strandMode = strandMode)
3: readGAlignmentPairs(bam, character(0), use.names = use.names, 
       param = param, with.which_label = with.which_label, strandMode = strandMode)
2: readGAlignmentPairs(bamFile, param = sbp)
1: readGAlignmentPairs(bamFile, param = sbp)

And my sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /software/free/r/R-3.4.0/lib/R/lib/libRblas.so
LAPACK: /software/free/r/R-3.4.0/lib/R/lib/libRlapack.so

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

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

other attached packages:
 [1] org.Hs.eg.db_3.4.1                      bedr_1.0.3                             
 [3] pbapply_1.3-3                           BSgenome.Hsapiens.UCSC.hg19_1.4.0      
 [5] BSgenome_1.44.0                         rtracklayer_1.36.3                     
 [7] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.28.4                 
 [9] AnnotationDbi_1.38.1                    GenomicAlignments_1.12.1               
[11] SummarizedExperiment_1.6.3              DelayedArray_0.2.7                     
[13] matrixStats_0.52.2                      Biobase_2.36.2                         
[15] Rsamtools_1.28.0                        Biostrings_2.44.1                      
[17] XVector_0.16.0                          GenomicRanges_1.28.3                   
[19] GenomeInfoDb_1.12.2                     IRanges_2.10.2                         
[21] S4Vectors_0.14.3                        BiocGenerics_0.22.0                    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11            futile.logger_1.4.3     compiler_3.4.0          R.methodsS3_1.7.1      
 [5] R.utils_2.5.0           futile.options_1.0.0    bitops_1.0-6            tools_3.4.0            
 [9] zlibbioc_1.22.0         testthat_1.0.2          biomaRt_2.32.1          digest_0.6.12          
[13] bit_1.1-12              RSQLite_2.0             memoise_1.1.0           tibble_1.3.3           
[17] lattice_0.20-35         pkgconfig_2.0.1         rlang_0.1.1             Matrix_1.2-10          
[21] DBI_0.7                 yaml_2.1.14             VennDiagram_1.6.17      GenomeInfoDbData_0.99.0
[25] bit64_0.9-7             grid_3.4.0              data.table_1.10.4       R6_2.2.2               
[29] XML_3.98-1.9            BiocParallel_1.10.1     magrittr_1.5            lambda.r_1.1.9         
[33] blob_1.1.0              RCurl_1.95-4.8          crayon_1.3.2            R.oo_1.21.0