public class CheckFingerprint extends CommandLineProgram
Modifier and Type | Field and Description |
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File |
DETAIL_OUTPUT |
String |
EXPECTED_SAMPLE_ALIAS |
static String |
FINGERPRINT_DETAIL_FILE_SUFFIX |
static String |
FINGERPRINT_SUMMARY_FILE_SUFFIX |
double |
GENOTYPE_LOD_THRESHOLD |
File |
GENOTYPES |
File |
HAPLOTYPE_MAP |
boolean |
IGNORE_READ_GROUPS |
File |
INPUT |
String |
OBSERVED_SAMPLE_ALIAS |
String |
OUTPUT |
File |
SUMMARY_OUTPUT |
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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CheckFingerprint() |
Modifier and Type | Method and Description |
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protected String[] |
customCommandLineValidation()
Put any custom command-line validation in an override of this method.
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protected int |
doWork()
Do the work after command line has been parsed.
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static void |
main(String[] args) |
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="I", doc="Input file SAM/BAM or VCF. If a VCF is used, it must have at least one sample. If there are more than one samples in the VCF, the parameter OBSERVED_SAMPLE_ALIAS must be provided in order to indicate which sample\'s data to use. If there are no samples in the VCF, an exception will be thrown.") public File INPUT
@Option(optional=true, doc="If the input is a VCF, this parameters used to select which sample\'s data in the VCF to use.") public String OBSERVED_SAMPLE_ALIAS
@Option(shortName="O", doc="The base prefix of output files to write. The summary metrics will have the file extension \'fingerprinting_summary_metrics\' and the detail metrics will have the extension \'fingerprinting_detail_metrics\'.", mutex={"SUMMARY_OUTPUT","DETAIL_OUTPUT"}) public String OUTPUT
@Option(shortName="S", doc="The text file to which to write summary metrics.", mutex="OUTPUT") public File SUMMARY_OUTPUT
@Option(shortName="D", doc="The text file to which to write detail metrics.", mutex="OUTPUT") public File DETAIL_OUTPUT
@Option(shortName="G", doc="File of genotypes (VCF or GELI) to be used in comparison. May contain any number of genotypes; CheckFingerprint will use only those that are usable for fingerprinting.") public File GENOTYPES
@Option(shortName="SAMPLE_ALIAS", optional=true, doc="This parameter can be used to specify which sample\'s genotypes to use from the expected VCF file (the GENOTYPES file). If it is not supplied, the sample name from the input (VCF or BAM read group header) will be used.") public String EXPECTED_SAMPLE_ALIAS
@Option(shortName="H", doc="A file of haplotype information produced by the CheckFingerprint program.") public File HAPLOTYPE_MAP
@Option(shortName="LOD", doc="When counting haplotypes checked and matching, count only haplotypes where the most likely haplotype achieves at least this LOD.") public double GENOTYPE_LOD_THRESHOLD
@Option(optional=true, shortName="IGNORE_RG", doc="If the input is a SAM/BAM, and this parameter is true, treat the entire input BAM as one single read group in the calculation, ignoring RG annotations, and producing a single fingerprint metric for the entire BAM.") public boolean IGNORE_READ_GROUPS
public static final String FINGERPRINT_SUMMARY_FILE_SUFFIX
public static final String FINGERPRINT_DETAIL_FILE_SUFFIX
public static void main(String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
protected String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram