Need BAM to BED algorithm

[jarwulf]

Hi, I've been looking for a good quick BAM to bed algorithm/code to integrate into a Java swing gui program. Usually we just use bedtools to do a simple nofrills conversion (no CIGAR or stuff like that) but there are many problems such incompatibility with windows. I've tried the bamtobed converter here

http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_protocol#Java_APIs_.28Picard.29

But I'm unsatisfied with the performance. I've thought about converting bedtool's bam converter to java myself but it looks extremely complicated with several files and multiple layers of dependencies. I was wondering if there was any java conversion of bedtools or any other code snippets I could try out.

Thanks

[Jim Robinson]

You should be able to build such a program using the Sam JDK in the Picard package. It would be straightforward, there are examples in the form of unit tests. You want to open a SAMFileReader, then use the "query" method to get an iterator over SAMRecord objects. The SAMRecord has all the info you need. Just remember the coordinates are "1" based and bed is "0".