public static class CollectQualityYieldMetrics.QualityYieldMetrics
extends htsjdk.samtools.metrics.MetricBase
Modifier and Type | Field | Description |
---|---|---|
long |
PF_BASES |
The total number of bases in all PF reads
|
long |
PF_Q20_BASES |
The number of bases in PF reads that achieve quality score 20 or higher
|
long |
PF_Q20_EQUIVALENT_YIELD |
The sum of quality scores of all bases divided by 20
|
long |
PF_Q30_BASES |
The number of bases in PF reads that achieve quality score 30 or higher
|
long |
PF_READS |
The number of reads that are PF - pass filter
|
long |
Q20_BASES |
The number of bases in all reads that achieve quality score 20 or higher
|
long |
Q20_EQUIVALENT_YIELD |
The sum of quality scores of all bases divided by 20
|
long |
Q30_BASES |
The number of bases in all reads that achieve quality score 30 or higher
|
int |
READ_LENGTH |
The average read length of all the reads (will be fixed for a lane)
|
long |
TOTAL_BASES |
The total number of bases in all reads
|
long |
TOTAL_READS |
The total number of reads in the input file
|
Constructor | Description |
---|---|
QualityYieldMetrics() |
public long TOTAL_READS
public long PF_READS
public int READ_LENGTH
public long TOTAL_BASES
public long PF_BASES
public long Q20_BASES
public long PF_Q20_BASES
public long Q30_BASES
public long PF_Q30_BASES
public long Q20_EQUIVALENT_YIELD
public long PF_Q20_EQUIVALENT_YIELD