Tagged with #qualifymissingintervals
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Hey guys -

We've started to play with QualifyMissingIntervals, and pretty quickly ran into a ReviewedStingException ("BED files must be parsed through Tribble; parsing them as intervals through the GATK engine is no longer supported") that confused us for a bit. We tracked it down to our use of bed files with the baits and targets arguments, and the use of IntervalUtils.intervalFileToList in the QMI initializer. We'll modify our reference files in the meantime, but could we request that those arguments use the interval parsing code used by -L? I think it's a relatively minor change, but I just don't have time to play with code right now (much less test it…)

Thanks!