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
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
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
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