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);
}
// -------------------------------------------------------------------------------------