[BioC] How to access custom SAM tags (Rsamtools?)

[Kemal Akman]

Hello,

I'm interested in accessing extended SAM tags in aligned short read
sequence files using a R/Bioconductor library. Rsamtools seems
potentially suited for this purpose, but I couldn't find the arguments
to return custom SAM tags, such as "XX:Z", but there doesn't seem to
be a corresponding "what" value in ScanBamParam()?

I'd be especially interested in such a feature to parse methylation
strings from Bismark, as well as custom SAM tags from other tools.

Any suggestions on Rsamtools or alternative methods to achieve this in
Bioconductor would be much appreciated.

Example SAM data:
$ head -2 sample.sam
SRR306424.2547_PRESLEY:4:4:62:558_length=76     16      chr22
30675421        255     36M     *       0       0
CACACACATCCACATAACACCATAACCAACCCCCGA
;,?A9:>B at B?@BBAC at C/BBC at CBCCC8BCBACBB    NM:i:4  XX:Z:15GG6G11G
XM:Z:...............hh......h..........Zx       XR:Z:CT XG:Z:GA
SRR306424.5227_PRESLEY:4:4:113:1768_length=76   0       chr5
123101409       255     75M     *       0       0
TGATTTTTATATAAGGTGTAAGTAAGAGGTTTAGTTTTGATTTTTTGTATATGGATAATTAGTTTTTTTAGTATT
    B>?@BBABBCBCCBCB>B at B@B?B at B@BB>BB at B?BBBB at BCBBABBAABABB@@B??ABAA>BABBBA=><@A=
    NM:i:13 XX:Z:22C8C12C4C8CC4C1CCC2C1CC
XM:Z:......................h........x............x....h........hx....h.hhx..h.hh
       XR:Z:CT XG:Z:CT


Best regards,

Kemal Akman