public final class RrbsSummaryMetrics extends MultilevelMetrics
Modifier and Type | Field and Description |
---|---|
java.lang.Integer |
CPG_BASES_CONVERTED
Number of CpG sites that were converted (TG for +, CA for -)
|
java.lang.Integer |
CPG_BASES_SEEN
Number of CpG sites encountered
|
java.lang.Double |
MEAN_CPG_COVERAGE
Mean coverage of CpG sites
|
java.lang.Integer |
MEDIAN_CPG_COVERAGE
Median coverage of CpG sites
|
java.lang.Integer |
NON_CPG_BASES
Number of times a non-CpG cytosine was encountered
|
java.lang.Integer |
NON_CPG_CONVERTED_BASES
Number of times a non-CpG cytosine was converted (C->T for +, G->A for -)
|
java.lang.Double |
PCT_CPG_BASES_CONVERTED
CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction)
|
java.lang.Double |
PCT_NON_CPG_BASES_CONVERTED
NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction)
|
java.lang.Integer |
READS_ALIGNED
Number of mapped reads processed
|
java.lang.Integer |
READS_IGNORED_MISMATCHES
Number of reads discarded for exceeding the mismatch threshold
|
java.lang.Integer |
READS_IGNORED_SHORT
Number of reads discarded due to being too short
|
java.lang.Integer |
READS_WITH_NO_CPG
Number of reads discarded for having no CpG sites
|
LIBRARY, READ_GROUP, SAMPLE
Constructor and Description |
---|
RrbsSummaryMetrics() |
public java.lang.Integer READS_ALIGNED
public java.lang.Integer NON_CPG_BASES
public java.lang.Integer NON_CPG_CONVERTED_BASES
public java.lang.Double PCT_NON_CPG_BASES_CONVERTED
public java.lang.Integer CPG_BASES_SEEN
public java.lang.Integer CPG_BASES_CONVERTED
public java.lang.Double PCT_CPG_BASES_CONVERTED
public java.lang.Double MEAN_CPG_COVERAGE
public java.lang.Integer MEDIAN_CPG_COVERAGE
public java.lang.Integer READS_WITH_NO_CPG
public java.lang.Integer READS_IGNORED_SHORT
public java.lang.Integer READS_IGNORED_MISMATCHES