Noticed that RSamtools::idxstatsBam() is not returning unmapped reads. When using bash samtools idxstats the last line reported is always a reference name of '*' and that line lists all the unmapped reads. That last line with reference name '*' does not show up when using RSamtools::idxstatsBam().

Reproducible example below uses a remote file, but same behavior is present if local bamfiles are used.

library(Rsamtools)
idxstatsBam("http://plantsmallrnagenes.science.psu.edu/bol-b1.0/alignments/SRR799356_3Q.bam")
  seqnames seqlength  mapped unmapped
1      C01  38761720 1091379        0
2      C02  44046003 1209217        0
3      C03  57781463 1763962        0
4      C04  40895475 2461661        0
5      C05  32828328 1657834        0
6      C06  40704471 1388970        0
7      C07  48346208 4523078        0
8      C08  41516064 3736635        0
9      C09  40126856 1518657        0

Compare to this:

# in bash
samtools idxstats http://plantsmallrnagenes.science.psu.edu/bol-b1.0/alignments/SRR799356_3Q.bam
C01 38761720    1091379 0
C02 44046003    1209217 0
C03 57781463    1763962 0
C04 40895475    2461661 0
C05 32828328    1657834 0
C06 40704471    1388970 0
C07 48346208    4523078 0
C08 41516064    3736635 0
C09 40126856    1518657 0
*   0   0   5517000

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] Rsamtools_2.4.0      Biostrings_2.56.0    XVector_0.28.0       GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 
[6] IRanges_2.22.2       S4Vectors_0.26.1     BiocGenerics_0.34.0 

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13        magrittr_2.0.1         knitr_1.31             zlibbioc_1.34.0       
 [5] BiocParallel_1.22.0    R6_2.5.0               rlang_0.4.10           stringr_1.4.0         
 [9] tools_4.0.2            xfun_0.22              tinytex_0.30           jquerylib_0.1.3       
[13] htmltools_0.5.1.1      yaml_2.2.1             digest_0.6.27          crayon_1.4.1          
[17] GenomeInfoDbData_1.2.3 sass_0.3.1             bitops_1.0-6           RCurl_1.98-1.3        
[21] evaluate_0.14          rmarkdown_2.7          stringi_1.5.3          compiler_4.0.2        
[25] bslib_0.2.4            jsonlite_1.7.2

This feature is available in Rsamtools 2.7.2. This requires use of R-4.1 / Bioconductor 3.13, and will be available in the next couple of days. Thanks for the request!