109 lines
4.1 KiB
Java
109 lines
4.1 KiB
Java
package edu.mit.broad.picard.directed;
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import edu.mit.broad.picard.metrics.MetricBase;
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/**
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* The set of metrics captured that are specific to a hybrid selection analysis.
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*
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* @author Tim Fennell
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*/
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public class HsMetrics extends MetricBase {
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/** The name of the bait set used in the hybrid selection. */
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public String BAIT_SET;
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/** The number of bases in the reference genome used for alignment. */
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public long GENOME_SIZE;
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/** The number of bases which have one or more baits on top of them. */
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public long BAIT_TERRITORY;
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/** The unique number of target bases in the experiment where target is usually exons etc. */
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public long TARGET_TERRITORY;
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/** Target terrirtoy / bait territory. 1 == perfectly efficient, 0.5 = half of baited bases are not target. */
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public double BAIT_DESIGN_EFFICIENCY;
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/** The total number of reads in the SAM or BAM file examine. */
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public int TOTAL_READS;
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/** The number of reads that pass the vendor's filter. */
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public int PF_READS;
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/** The number of PF reads that are not marked as duplicates. */
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public int PF_UNIQUE_READS;
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/** PF reads / total reads. The percent of reads passing filter. */
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public double PCT_PF_READS;
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/** PF Unique Reads / Total Reads. */
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public double PCT_PF_UQ_READS;
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/** The number of PF reads that are aligned with mapping score > 0 to the reference genome. */
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public int PF_READS_ALIGNED;
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/** PF Reads Aligned / PF Reads. */
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public double PCT_PF_READS_ALIGNED;
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/** The number of bases in the PF aligned reads that are mapped to a reference base. Accounts for clipping and gaps. */
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public int PF_BASES_ALIGNED;
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/** The number of PF aligned bases that mapped to a baited region of the genome. */
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public long ON_BAIT_BASES;
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/** The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region. */
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public long NEAR_BAIT_BASES;
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/** The number of PF aligned bases that mapped to neither on or near a bait. */
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public long OFF_BAIT_BASES;
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/** The number of PF aligned bases that mapped to a targetted region of the genome. */
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public long ON_TARGET_BASES;
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/** On+Near Bait Bases / PF Bases Aligned. */
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public double PCT_SELECTED_BASES;
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/** The percentage of aligned PF bases that mapped neither on or near a bait. */
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public double PCT_OFF_BAIT;
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/** The percentage of on+near bait bases that are on as opposed to near. */
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public double ON_BAIT_VS_SELECTED;
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/** The mean coverage of all baits in the experiment. */
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public double MEAN_BAIT_COVERAGE;
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/** The mean coverage of targets that recieved at least coverage depth = 2 at one base. */
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public double MEAN_TARGET_COVERAGE;
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/** The fold by which the baited region has been amplified above genomic background. */
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public double FOLD_ENRICHMENT;
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/** The number of targets that did not reach coverage=2 over any base. */
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public double ZERO_CVG_TARGETS_PCT;
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/**
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* The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to
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* the mean coverage level in those targets.
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*/
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public double FOLD_80_BASE_PENALTY;
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/**
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* Calculates the metrics in this class that can be derived from other metrics in the class.
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*/
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public void calculateDerivedMetrics() {
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BAIT_DESIGN_EFFICIENCY = (double) TARGET_TERRITORY / (double) BAIT_TERRITORY;
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PCT_PF_READS = PF_READS / (double) TOTAL_READS;
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PCT_PF_UQ_READS = PF_UNIQUE_READS / (double) TOTAL_READS;
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PCT_PF_READS_ALIGNED = PF_READS_ALIGNED / (double) PF_UNIQUE_READS;
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double denominator = (ON_BAIT_BASES + NEAR_BAIT_BASES + OFF_BAIT_BASES);
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PCT_SELECTED_BASES = (ON_BAIT_BASES + NEAR_BAIT_BASES) / denominator;
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PCT_OFF_BAIT = OFF_BAIT_BASES / denominator;
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ON_BAIT_VS_SELECTED = ON_BAIT_BASES / (double) (ON_BAIT_BASES + NEAR_BAIT_BASES);
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MEAN_BAIT_COVERAGE = ON_BAIT_BASES / (double) BAIT_TERRITORY;
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FOLD_ENRICHMENT = (ON_BAIT_BASES/ denominator) / ((double) BAIT_TERRITORY / GENOME_SIZE);
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}
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}
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