CalculateHsMetrics
public class CollectHsMetrics extends CollectTargetedMetrics<HsMetrics,HsMetricCollector>
Modifier and Type | Field | Description |
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List<File> |
BAIT_INTERVALS |
|
String |
BAIT_SET_NAME |
|
boolean |
CLIP_OVERLAPPING_READS |
|
int |
MINIMUM_BASE_QUALITY |
|
int |
MINIMUM_MAPPING_QUALITY |
COVERAGE_CAP, INPUT, METRIC_ACCUMULATION_LEVEL, NEAR_DISTANCE, OUTPUT, PER_BASE_COVERAGE, PER_TARGET_COVERAGE, SAMPLE_SIZE, TARGET_INTERVALS
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor | Description |
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CollectHsMetrics() |
Modifier and Type | Method | Description |
---|---|---|
protected htsjdk.samtools.util.IntervalList |
getProbeIntervals() |
|
protected String |
getProbeSetName() |
|
static void |
main(String[] argv) |
Stock main method.
|
protected HsMetricCollector |
makeCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
htsjdk.samtools.reference.ReferenceSequenceFile refFile,
File perTargetCoverage,
File perBaseCoverage,
htsjdk.samtools.util.IntervalList targetIntervals,
htsjdk.samtools.util.IntervalList probeIntervals,
String probeSetName,
int nearProbeDistance) |
A factory method for the TargetMetricsCollector to use this time.
|
customCommandLineValidation, doWork
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="BI", doc="An interval list file that contains the locations of the baits used.", minElements=1) public List<File> BAIT_INTERVALS
@Option(shortName="N", doc="Bait set name. If not provided it is inferred from the filename of the bait intervals.", optional=true) public String BAIT_SET_NAME
@Option(shortName="MQ", doc="Minimum mapping quality for a read to contribute coverage.", overridable=true) public int MINIMUM_MAPPING_QUALITY
@Option(shortName="Q", doc="Minimum base quality for a base to contribute coverage.", overridable=true) public int MINIMUM_BASE_QUALITY
@Option(doc="True if we are to clip overlapping reads, false otherwise.", optional=true, overridable=true) public boolean CLIP_OVERLAPPING_READS
protected htsjdk.samtools.util.IntervalList getProbeIntervals()
getProbeIntervals
in class CollectTargetedMetrics<HsMetrics,HsMetricCollector>
protected String getProbeSetName()
getProbeSetName
in class CollectTargetedMetrics<HsMetrics,HsMetricCollector>
public static void main(String[] argv)
protected HsMetricCollector makeCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, File perTargetCoverage, File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, String probeSetName, int nearProbeDistance)
CollectTargetedMetrics
makeCollector
in class CollectTargetedMetrics<HsMetrics,HsMetricCollector>