package picard.analysis.directed;
import picard.metrics.MultilevelMetrics;
/** Metrics class for targeted pcr runs such as TSCA runs */
public class TargetedPcrMetrics extends MultilevelMetrics {
/** The name of the amplicon set used in this metrics collection run */
public String CUSTOM_AMPLICON_SET;
/** The number of bases in the reference genome used for alignment. */
public long GENOME_SIZE;
/** The number of unique bases covered by the intervals of all amplicons in the amplicon set */
public long AMPLICON_TERRITORY;
/** The number of unique bases covered by the intervals of all targets that should be covered */
public long TARGET_TERRITORY;
/** The total number of reads in the SAM or BAM file examine. */
public long TOTAL_READS;
/** The number of reads that pass the vendor's filter. */
public long PF_READS;
/** THe number of bases in the SAM or BAM file to be examined */
public long PF_BASES;
/** The number of PF reads that are not marked as duplicates. */
public long PF_UNIQUE_READS;
/** PF reads / total reads. The percent of reads passing filter. */
public double PCT_PF_READS;
/** PF Unique Reads / Total Reads. */
public double PCT_PF_UQ_READS;
/** The number of PF unique reads that are aligned with mapping score > 0 to the reference genome. */
public long PF_UQ_READS_ALIGNED;
/** Tracks the number of read pairs that we see that are PF (used to calculate library size) */
public long PF_SELECTED_PAIRS;
/** Tracks the number of unique PF reads pairs we see (used to calc library size) */
public long PF_SELECTED_UNIQUE_PAIRS;
/** PF Reads Aligned / PF Reads. */
public double PCT_PF_UQ_READS_ALIGNED;
/** The number of PF unique bases that are aligned with mapping score > 0 to the reference genome. */
public long PF_UQ_BASES_ALIGNED;
/** The number of PF aligned amplified that mapped to an amplified region of the genome. */
public long ON_AMPLICON_BASES;
/** The number of PF aligned bases that mapped to within a fixed interval of an amplified region, but not on a baited region. */
public long NEAR_AMPLICON_BASES;
/** The number of PF aligned bases that mapped to neither on or near an amplicon. */
public long OFF_AMPLICON_BASES;
/** The number of PF aligned bases that mapped to a targeted region of the genome. */
public long ON_TARGET_BASES;
/** The number of PF aligned bases that are mapped in pair to a targeted region of the genome. */
public long ON_TARGET_FROM_PAIR_BASES;
/** On+Near Amplicon Bases / PF Bases Aligned. */
public double PCT_AMPLIFIED_BASES;
/** The percentage of aligned PF bases that mapped neither on or near an amplicon. */
public double PCT_OFF_AMPLICON;
/** The percentage of on+near amplicon bases that are on as opposed to near. */
public double ON_AMPLICON_VS_SELECTED;
/** The mean coverage of all amplicons in the experiment. */
public double MEAN_AMPLICON_COVERAGE;
/** The mean coverage of targets that recieved at least coverage depth = 2 at one base. */
public double MEAN_TARGET_COVERAGE;
/** The fold by which the amplicon region has been amplified above genomic background. */
public double FOLD_ENRICHMENT;
/** The number of targets that did not reach coverage=2 over any base. */
public double ZERO_CVG_TARGETS_PCT;
/**
* The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to
* the mean coverage level in those targets.
*/
public double FOLD_80_BASE_PENALTY;
/** The percentage of ALL target bases achieving 2X or greater coverage. */
public double PCT_TARGET_BASES_2X;
/** The percentage of ALL target bases achieving 10X or greater coverage. */
public double PCT_TARGET_BASES_10X;
/** The percentage of ALL target bases achieving 20X or greater coverage. */
public double PCT_TARGET_BASES_20X;
/** The percentage of ALL target bases achieving 30X or greater coverage. */
public double PCT_TARGET_BASES_30X;
/**
* A measure of how undercovered <= 50% GC regions are relative to the mean. For each GC bin [0..50]
* we calculate a = % of target territory, and b = % of aligned reads aligned to these targets.
* AT DROPOUT is then abs(sum(a-b when a-b < 0)). E.g. if the value is 5% this implies that 5% of total
* reads that should have mapped to GC<=50% regions mapped elsewhere.
*/
public double AT_DROPOUT;
/**
* A measure of how undercovered >= 50% GC regions are relative to the mean. For each GC bin [50..100]
* we calculate a = % of target territory, and b = % of aligned reads aligned to these targets.
* GC DROPOUT is then abs(sum(a-b when a-b < 0)). E.g. if the value is 5% this implies that 5% of total
* reads that should have mapped to GC>=50% regions mapped elsewhere.
*/
public double GC_DROPOUT;
}