How to get the identity of an indel in pileup

[kentwait]

Is there a way to get the inserted or deleted sequence while doing a pileup?

For example the reference is the first line and there are 3 mapped reads.
The first read has an insertion GGC and the third has a deletion of GGC.

ref:   GCGGGCGGCTCTTATATTATAAAGAGCTAGAATATCG
read1: GCGGGCGGC[GGC]TCTTATATTATAAAGAGCTAGAATATCG
read2: GCGGGCGGCTCTTATATTATAAAGAGCTAGAATATCG
read3: GCGGGC---TCTTATATTATAAAGAGCTAGAATATCG

Using the example code below will get the length of the indel (3) but I don't know how to get the inserted or deleted bases.

// mark indel start
match alignment.indel() {
    bam::pileup::Indel::Ins(len) => println!("Insertion of length {} between this and next position.", len),
    bam::pileup::Indel::Del(len) => println!("Deletion of length {} between this and next position.", len),
    bam::pileup::Indel::None => ()
}

In samtools mpileup this would be +3GGC for insertion or -3GGC for deletion. Is there an existing method for this or do I need to manually process this by reading the CIGAR of each read?

Thank you for the help.

[ebioman]

Hi @kentwait
I have currently the same problem, did you solve this by chance ?
thx