public class CollectRrbsMetrics extends CommandLineProgram
Modifier and Type | Field and Description |
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boolean |
ASSUME_SORTED |
int |
C_QUALITY_THRESHOLD |
static java.lang.String |
DETAIL_FILE_EXTENSION |
java.io.File |
INPUT |
double |
MAX_MISMATCH_RATE |
java.util.Set<MetricAccumulationLevel> |
METRIC_ACCUMULATION_LEVEL |
java.lang.String |
METRICS_FILE_PREFIX |
int |
MINIMUM_READ_LENGTH |
int |
NEXT_BASE_QUALITY_THRESHOLD |
static java.lang.String |
PDF_FILE_EXTENSION |
java.io.File |
REFERENCE |
java.util.Set<java.lang.String> |
SEQUENCE_NAMES |
static java.lang.String |
SUMMARY_FILE_EXTENSION |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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CollectRrbsMetrics() |
Modifier and Type | Method and Description |
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protected java.lang.String[] |
customCommandLineValidation()
Put any custom command-line validation in an override of this method.
|
protected int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(java.lang.String[] args) |
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(doc="The BAM or SAM file containing aligned reads. Must be coordinate sorted", shortName="I") public java.io.File INPUT
@Option(doc="Base name for output files", shortName="M") public java.lang.String METRICS_FILE_PREFIX
@Option(doc="The reference sequence fasta file", shortName="R") public java.io.File REFERENCE
@Option(doc="Threshold for base quality of a C base before it is considered") public int C_QUALITY_THRESHOLD
@Option(doc="Threshold for quality of a base next to a C before the C base is considered") public int NEXT_BASE_QUALITY_THRESHOLD
@Option(doc="Maximum percentage of mismatches in a read for it to be considered, with a range of 0-1") public double MAX_MISMATCH_RATE
@Option(doc="Set of sequence names to consider, if not specified all sequences will be used", optional=true) public java.util.Set<java.lang.String> SEQUENCE_NAMES
@Option(shortName="AS", doc="If true, assume that the input file is coordinate sorted even if the header says otherwise.") public boolean ASSUME_SORTED
@Option(shortName="LEVEL", doc="The level(s) at which to accumulate metrics. ") public java.util.Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL
public static final java.lang.String DETAIL_FILE_EXTENSION
public static final java.lang.String SUMMARY_FILE_EXTENSION
public static final java.lang.String PDF_FILE_EXTENSION
public static void main(java.lang.String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
protected java.lang.String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram