java parser for bed file

Question

[alex]

Hi everyone,

I am looking for a bed file parser in java. I've done a look through htsjdk and there doesn't appear to be one. There does appear to be one for IntervalList files, but that's not what I have and would prefer not to go through the conversion process. I've looked at How Could I Handle Bed Files In Java? but that doesn't seem to have a nice solution on how to parse a file and get a java object that can be manipulated. Any thoughts? Thanks!

[Pierre Lindenbaum]

please define "that can be manipulated", and there's one in htsjdk: https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/tribble/bed/BEDCodec.java