Fix performance issue where debug code was left in production #315
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The expected names of cram/bam files associated with ancillary files are known, so there is no need to repeatedly iterate the collections. Also, associateion of a stem with a cram/bam file can be cached.
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The expected names of cram/bam files associated with ancillary files are known, so there is no need to repeatedly iterate the collections. Also, associateion of a stem with a cram/bam file can be cached.