MethylR on bam files Gives Error

Question

[anasjamshed]

I used bismark to get bam files and now trying to implement processBismarkAln() on it but getting the following error:

Using htslib.
Error: Unexpected cigar: M

As far as I know, some possible causes of this error could include:

1)A problem with the software or pipeline used to generate the BAM file

2)Errors or inconsistencies in the reference genome used for the alignment

3)Issues with the alignment algorithm or parameters used

How can I resolve this issue? Do I need to open sam files in text editor and make changes?