/*
* The MIT License
*
* Copyright (c) 2009 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.analysis;
import htsjdk.samtools.SamPairUtil.PairOrientation;
import picard.metrics.MultilevelMetrics;
/**
* Metrics about the insert size distribution of a paired-end library, created by the
* CollectInsertSizeMetrics program and usually written to a file with the extension
* ".insert_size_metrics". In addition the insert size distribution is plotted to
* a file with the extension ".insert_size_Histogram.pdf".
*
* @author Doug Voet (dvoet at broadinstitute dot org)
*/
public class InsertSizeMetrics extends MultilevelMetrics {
/** The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome. */
public double MEDIAN_INSERT_SIZE;
/**
* The median absolute deviation of the distribution. If the distribution is essentially normal then
* the standard deviation can be estimated as ~1.4826 * MAD.
*/
public double MEDIAN_ABSOLUTE_DEVIATION;
/** The minimum measured insert size. This is usually 1 and not very useful as it is likely artifactual. */
public int MIN_INSERT_SIZE;
/**
* The maximum measure insert size by alignment. This is usually very high representing either an artifact
* or possibly the presence of a structural re-arrangement.
*/
public int MAX_INSERT_SIZE;
/**
* The mean insert size of the "core" of the distribution. Artefactual outliers in the distribution often
* cause calculation of nonsensical mean and stdev values. To avoid this the distribution is first trimmed
* to a "core" distribution of +/- N median absolute deviations around the median insert size. By default
* N=10, but this is configurable.
*/
public double MEAN_INSERT_SIZE;
/** Standard deviation of insert sizes over the "core" of the distribution. */
public double STANDARD_DEVIATION;
/** The total number of read pairs that were examined in the entire distribution. */
public long READ_PAIRS;
/** The pair orientation of the reads in this data category. */
public PairOrientation PAIR_ORIENTATION;
/** The "width" of the bins, centered around the median, that encompass 10% of all read pairs. */
public int WIDTH_OF_10_PERCENT;
/** The "width" of the bins, centered around the median, that encompass 20% of all read pairs. */
public int WIDTH_OF_20_PERCENT;
/** The "width" of the bins, centered around the median, that encompass 30% of all read pairs. */
public int WIDTH_OF_30_PERCENT;
/** The "width" of the bins, centered around the median, that encompass 40% of all read pairs. */
public int WIDTH_OF_40_PERCENT;
/** The "width" of the bins, centered around the median, that encompass 50% of all read pairs. */
public int WIDTH_OF_50_PERCENT;
/** The "width" of the bins, centered around the median, that encompass 60% of all read pairs. */
public int WIDTH_OF_60_PERCENT;
/**
* The "width" of the bins, centered around the median, that encompass 70% of all read pairs.
* This metric divided by 2 should approximate the standard deviation when the insert size
* distribution is a normal distribution.
*/
public int WIDTH_OF_70_PERCENT;
/** The "width" of the bins, centered around the median, that encompass 80% of all read pairs. */
public int WIDTH_OF_80_PERCENT;
/** The "width" of the bins, centered around the median, that encompass 90% of all read pairs. */
public int WIDTH_OF_90_PERCENT;
/** The "width" of the bins, centered around the median, that encompass 100% of all read pairs. */
public int WIDTH_OF_99_PERCENT;
}