Dear all,

We are processing long reads from Oxford Nanopore and we are in need to parse both secondary alignments (SAM flag 0x100) and the supplementary alignments (SAM flag 0x800) from their primary and representative alignments. 

From Rsamtools, scanBamFlag() allows for parsing the secondary [0x100, i.e. isSecondaryAlignment=c(TRUE,FALSE,NA)] from the rest but I can't find any flag that would allow us to retrieve the supplementary entries. 

Am I missing something? Any help would be greatly appreciated.

Thanks, its surprising that this hasn't come up before, and that it has not been implemented. This will be available via a flag isSupplementaryAlignment in Rsamtools version 1.32.3 (Bioconductor version 3.7) / 1.33.4 (devel) in the next day or so; it can also be installed using BiocManager::install("Bioconductor/Rsamtools", ref = "RELEASE_3_7") (or ref = "master" for devel) now.