Parsing SAM files with java

Question

[Matej]

Hello, I'm working on a java program that has to make use of SAM files, is there a relatively painless way to load SAM files and parse them? I've been using BioJava for FASTA files but as far as I can understand there is nothing on SAM files in BioJava. Any pointers would be helpful.

[cmdcolin]

one thing that may be of interest: SAM files are plaintext, some basic operations can be done with very basic text operations so it may depend on your needs whether you need to parse the data with a sophisticated library

Answer 1

[Pierre Lindenbaum]

duplicate: Reading .sam files in java