BAM to Bed Algorithm

[jarwulf]

Hi, I'm looking for an algorithm/code I can use to convert BAM files to bed that I can stick in a C++ file. Preferably something that is generic/works for windows. I'm looking through bedtools but that only works for Unix/Apple so its harder to understand with all the added dependencies and other features bolted on and the inability to build/run it on my system natively (at least without a lot of hassle and additional downloading).

[arvid]

If you are not ready to tackle the samtools library (there should be a Windows port, search for it in the forum) and make the BED writer yourself (that part should be simple, though, the BED format isn't that complicated), you could use the Picard library for parsing BAM (in Java, however, and you still need to make a BED writer).

IMHO, I wouldn't start rewriting all the tools to fit them to the platform I use, rather get a platform-independent setup to be able to build and run all tools natively. In your case this means to get a cygwin installation if you only casually need Unix command line tools, or a virtual machine with Linux. I guess BEDtools won't be the only tool made for Unix you'll come across in the near future, if you're working with NGS data...