if ( this.walker.wantsExtendedReads() && ! this.walker.wantsNonPrimaryReads() ) {
throw new IllegalArgumentException("Active region walker " + this.walker + " requested extended events but not " +
"non-primary reads, an inconsistent state. Please modify the walker");
}
ActiveRegionTraversalParameters annotation = walker.getClass().getAnnotation(ActiveRegionTraversalParameters.class);
this.activeRegionExtension = this.walker.activeRegionExtension == null ? annotation.extension() : this.walker.activeRegionExtension;
this.maxRegionSize = this.walker.activeRegionMaxSize == null ? annotation.maxRegion() : this.walker.activeRegionMaxSize;
this.minRegionSize = annotation.minRegion();
final double bandPassSigma = this.walker.bandPassSigma == null ? annotation.bandPassSigma() : this.walker.bandPassSigma;
walkerHasPresetRegions = this.walker.hasPresetActiveRegions();
activityProfile = new BandPassActivityProfile(engine.getGenomeLocParser(), engine.getIntervals(), this.walker.maxProbPropagationDistance, this.walker.activeProbThreshold,
BandPassActivityProfile.MAX_FILTER_SIZE, bandPassSigma);
final int maxReadsAcrossSamples = annotation.maxReadsToHoldInMemoryPerSample() * SampleUtils.getSAMFileSamples(engine).size();
final int maxReadsToHoldInMemory = Math.min(maxReadsAcrossSamples, annotation.maxReadsToHoldTotal());
myReads = new TAROrderedReadCache(maxReadsToHoldInMemory);
}