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picard.util.IntervalList.IntervalListScattererByIntervalCount Maven / Gradle / Ivy
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/*
* The MIT License
*
* Copyright (c) 2018 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.util.IntervalList;
import htsjdk.samtools.util.CollectionUtil;
import htsjdk.samtools.util.Interval;
import htsjdk.samtools.util.IntervalList;
import java.util.Arrays;
import java.util.List;
/**
* Scatters {@link IntervalList} by interval count so that resulting {@link IntervalList}'s have the same number of intervals in them.
* An exception is made for the final interval list, which will always contain at least this number of intervals,
* but may also contain the remainder.
*/
public class IntervalListScattererByIntervalCount implements IntervalListScatterer {
@Override
public long intervalWeight(final Interval interval) {
return 1;
}
@Override
public long listWeight(final IntervalList intervalList) {
return intervalList.size();
}
@Override
public List takeSome(final Interval interval, final long idealSplitWeight, final long currentSize, final double projectSizeOfRemaining) {
final long amount = idealSplitWeight - currentSize;
if (amount > 0) {
return Arrays.asList(interval, null);
} else {
return Arrays.asList(null, interval);
}
}
@Override
public int deduceIdealSplitWeight(final IntervalList intervalList, final int nCount) {
return (int) Math.max(1, Math.floorDiv(listWeight(intervalList), nCount));
}
}
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