org.broadinstitute.hellbender.metrics.InsertSizeMetrics Maven / Gradle / Ivy
package org.broadinstitute.hellbender.metrics;
import htsjdk.samtools.SamPairUtil.PairOrientation;
import org.broadinstitute.hellbender.metrics.MultiLevelMetrics;
import java.io.Serializable;
/**
* 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
* ".insertSizeMetrics". In addition the insert size distribution is plotted to
* a file with the extension ".insertSizeMetrics.pdf".
*/
public final class InsertSizeMetrics extends MultiLevelMetrics implements Serializable {
private static final long serialVersionUID = 1L;
/**
* 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;
/**
* Return a disambiguating name suffix to be used by the multiple collectors to
* decorate output names, which are provided by the user in the form of a base name
* that needs to be disambiguated for each individual collector. This prevents
* a collector from clobbering the previous collectors output file(s). The value
* is not used here.
*/
public static String getUniqueNameSuffix() { return "insertSizeMetrics";}
}