Stand-alone utility for filtering a BAM file to specific genomic regions, using Apache Spark.
sbt assembly spark-submit \ --properties-file <spark properties file> \ target/scala-2.11/filter-bam-assembly-1.0.0-SNAPSHOT.jar \ in.bam \ <regions> \ out.bam \ [-c] [--include-unmapped-mates]
<regions>: comma-separated list of genomic regions, in the format accepted by
--count: print the number of reads output, in addition to writing
--include-unmapped-mates: include unmapped reads whose mate-contig and mate-start are set to a value that overlaps