case class AssessPhasingMetric(num_called: Long = 0, num_phased: Long = 0, num_truth: Long = 0, num_truth_phased: Long = 0, num_called_with_truth_phased: Long = 0, num_phased_with_truth_phased: Long = 0, num_truth_phased_in_called_block: Long = 0, num_both_phased_in_called_block: Long = 0, num_short_switch_errors: Long = 0, num_long_switch_errors: Long = 0, num_switch_sites: Long = 0, num_illumina_point_switch_errors: Long = 0, num_illumina_long_switch_errors: Long = 0, num_illumina_switch_sites: Long = 0, frac_phased: Double = 0, frac_phased_with_truth_phased: Double = 0, frac_truth_phased_in_called_block: Double = 0, frac_phased_with_truth_phased_in_called_block: Double = 0, short_accuracy: Double = 0, long_accuracy: Double = 0, illumina_point_accuracy: Double = 0, illumina_long_accuracy: Double = 0, mean_called_block_length: Double = 0, median_called_block_length: Double = 0, stddev_called_block_length: Double = 0, n50_called_block_length: Double = 0, n90_called_block_length: Double = 0, l50_called: Double = 0, mean_truth_block_length: Double = 0, median_truth_block_length: Double = 0, stddev_truth_block_length: Double = 0, n50_truth_block_length: Double = 0, n90_truth_block_length: Double = 0, l50_truth: Double = 0) extends Metric with Product with Serializable
Some counts about phasing
- num_called
the number of variants called.
- num_phased
the number of variants called with phase.
- num_truth
the number of variants with known truth genotypes.
- num_truth_phased
the number of variants with known truth genotypes with phase.
- num_called_with_truth_phased
the number of variants called that had a known phased genotype.
- num_phased_with_truth_phased
the number of variants called with phase that had a known phased genotype.
- num_truth_phased_in_called_block
the number of known phased variants that were in a called phased block.
- num_both_phased_in_called_block
the number of called phase variants that had a known phased genotype in a called phased block.
- num_short_switch_errors
the number of short switch errors (isolated switch errors).
- num_long_switch_errors
the number of long switch errors (# of runs of consecutive switch errors).
- num_switch_sites
the number of sites that could be (short or long) switch errors (i.e. the # of sites with both known and called phased variants).
- num_illumina_point_switch_errors
the number of point switch errors (defined in http://dx.doi.org/10.1038%2Fng.3119).
- num_illumina_long_switch_errors
the number of long switch errors (defined in http://dx.doi.org/10.1038%2Fng.3119).
- num_illumina_switch_sites
the number of sites that could be (point or long) switch errors (defined in http://dx.doi.org/10.1038%2Fng.3119).
- frac_phased
the fraction of called variants with phase.
- frac_phased_with_truth_phased
the fraction of known phased variants called with phase.
- frac_truth_phased_in_called_block
the fraction of phased known genotypes in a called phased block.
- frac_phased_with_truth_phased_in_called_block
the fraction of called phased variants that had a known phased genotype in a called phased block.
- short_accuracy
1 - (num_short_switch_errors / num_switch_sites)
- long_accuracy
1 - (num_long_switch_errors / num_switch_sites)
- illumina_point_accuracy
1 - (num_illumina_point_switch_errors / num_illumina_switch_sites )
- illumina_long_accuracy
1 - (num_illumina_long_switch_errors / num_illumina_switch_sites )
- mean_called_block_length
the mean phased block length in the callset.
- median_called_block_length
the median phased block length in the callset.
- stddev_called_block_length
the standard deviation of the phased block length in the callset.
- n50_called_block_length
the N50 of the phased block length in the callset.
- n90_called_block_length
the N90 of the phased block length in the callset.
- l50_called
the L50 of the phased block length in the callset.
- mean_truth_block_length
the mean phased block length in the truth.
- median_truth_block_length
the median phased block length in the truth.
- stddev_truth_block_length
the standard deviation of the phased block length in the truth.
- n50_truth_block_length
the N50 of the phased block length in the truth.
- n90_truth_block_length
the N90 of the phased block length in the callset.
- l50_truth
the L50 of the phased block length in the callset.
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new
AssessPhasingMetric(num_called: Long = 0, num_phased: Long = 0, num_truth: Long = 0, num_truth_phased: Long = 0, num_called_with_truth_phased: Long = 0, num_phased_with_truth_phased: Long = 0, num_truth_phased_in_called_block: Long = 0, num_both_phased_in_called_block: Long = 0, num_short_switch_errors: Long = 0, num_long_switch_errors: Long = 0, num_switch_sites: Long = 0, num_illumina_point_switch_errors: Long = 0, num_illumina_long_switch_errors: Long = 0, num_illumina_switch_sites: Long = 0, frac_phased: Double = 0, frac_phased_with_truth_phased: Double = 0, frac_truth_phased_in_called_block: Double = 0, frac_phased_with_truth_phased_in_called_block: Double = 0, short_accuracy: Double = 0, long_accuracy: Double = 0, illumina_point_accuracy: Double = 0, illumina_long_accuracy: Double = 0, mean_called_block_length: Double = 0, median_called_block_length: Double = 0, stddev_called_block_length: Double = 0, n50_called_block_length: Double = 0, n90_called_block_length: Double = 0, l50_called: Double = 0, mean_truth_block_length: Double = 0, median_truth_block_length: Double = 0, stddev_truth_block_length: Double = 0, n50_truth_block_length: Double = 0, n90_truth_block_length: Double = 0, l50_truth: Double = 0)
- num_called
the number of variants called.
- num_phased
the number of variants called with phase.
- num_truth
the number of variants with known truth genotypes.
- num_truth_phased
the number of variants with known truth genotypes with phase.
- num_called_with_truth_phased
the number of variants called that had a known phased genotype.
- num_phased_with_truth_phased
the number of variants called with phase that had a known phased genotype.
- num_truth_phased_in_called_block
the number of known phased variants that were in a called phased block.
- num_both_phased_in_called_block
the number of called phase variants that had a known phased genotype in a called phased block.
- num_short_switch_errors
the number of short switch errors (isolated switch errors).
- num_long_switch_errors
the number of long switch errors (# of runs of consecutive switch errors).
- num_switch_sites
the number of sites that could be (short or long) switch errors (i.e. the # of sites with both known and called phased variants).
- num_illumina_point_switch_errors
the number of point switch errors (defined in http://dx.doi.org/10.1038%2Fng.3119).
- num_illumina_long_switch_errors
the number of long switch errors (defined in http://dx.doi.org/10.1038%2Fng.3119).
- num_illumina_switch_sites
the number of sites that could be (point or long) switch errors (defined in http://dx.doi.org/10.1038%2Fng.3119).
- frac_phased
the fraction of called variants with phase.
- frac_phased_with_truth_phased
the fraction of known phased variants called with phase.
- frac_truth_phased_in_called_block
the fraction of phased known genotypes in a called phased block.
- frac_phased_with_truth_phased_in_called_block
the fraction of called phased variants that had a known phased genotype in a called phased block.
- short_accuracy
1 - (num_short_switch_errors / num_switch_sites)
- long_accuracy
1 - (num_long_switch_errors / num_switch_sites)
- illumina_point_accuracy
1 - (num_illumina_point_switch_errors / num_illumina_switch_sites )
- illumina_long_accuracy
1 - (num_illumina_long_switch_errors / num_illumina_switch_sites )
- mean_called_block_length
the mean phased block length in the callset.
- median_called_block_length
the median phased block length in the callset.
- stddev_called_block_length
the standard deviation of the phased block length in the callset.
- n50_called_block_length
the N50 of the phased block length in the callset.
- n90_called_block_length
the N90 of the phased block length in the callset.
- l50_called
the L50 of the phased block length in the callset.
- mean_truth_block_length
the mean phased block length in the truth.
- median_truth_block_length
the median phased block length in the truth.
- stddev_truth_block_length
the standard deviation of the phased block length in the truth.
- n50_truth_block_length
the N50 of the phased block length in the truth.
- n90_truth_block_length
the N90 of the phased block length in the callset.
- l50_truth
the L50 of the phased block length in the callset.
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- var frac_phased: Double
- var frac_phased_with_truth_phased: Double
- var frac_phased_with_truth_phased_in_called_block: Double
- var frac_truth_phased_in_called_block: Double
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- var l50_called: Double
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- var median_called_block_length: Double
- var median_truth_block_length: Double
- var n50_called_block_length: Double
- var n50_truth_block_length: Double
- var n90_called_block_length: Double
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- var num_both_phased_in_called_block: Long
- var num_called: Long
- var num_called_with_truth_phased: Long
- var num_illumina_long_switch_errors: Long
- var num_illumina_point_switch_errors: Long
- var num_illumina_switch_sites: Long
- var num_long_switch_errors: Long
- var num_phased: Long
- var num_phased_with_truth_phased: Long
- var num_short_switch_errors: Long
- var num_switch_sites: Long
- var num_truth: Long
- var num_truth_phased: Long
- var num_truth_phased_in_called_block: Long
- var short_accuracy: Double
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