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Cascalog based approach for BioStar question about comparing intervals from two BED files stored in HDFS. Install:

Then run:

    % lein deps
    % lein uberjar
    % hadoop fs -mkdir /tmp/bed-hadoop/bed-1
    % hadoop fs -mkdir /tmp/bed-hadoop/bed-2
    % hadoop fs -put test/one.bed /tmp/bed-hadoop/bed-1
    % hadoop fs -put test/two.bed /tmp/bed-hadoop/bed-2
    % hadoop jar bed-hadoop-0.0.1-SNAPSHOT-standalone.jar
                 bed_hadoop.core /tmp/bed-hadoop/bed-1 /tmp/bed-hadoop/bed-2
    chr1 20 30
    chr2 40 50
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