I have a .sam file (for single-end reads) and I wish to find the end position of each read. I noticed that I can do that using Rsamtools if the file is a .bam file. However, I wish to do it directly on .sam file. How should I do? (using cigar value?)

Thanks!

You could read the start and cigar from the SAM file using standard R or other (e.g., readr) facilities (probably important to read only the relevant columns, for performance) then use GenomicAlignments::cigarWidthAlongReferenceSpace() and similar.

If  you want to parse a text file, you are probably better off just using perl or awk. You could do this in R, but it's not really designed for fast parsing of text files.

Thanks for both answers!