public class CheckFingerprint extends CommandLineProgram
Modifier and Type | Field and Description |
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File |
DETAIL_OUTPUT |
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 |
OUTPUT |
String |
SAMPLE_ALIAS |
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 int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="O", doc="The base 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(optional=true, doc="If using VCF format genotypes, this parameter can be used to specify which sample\'s genotypes to use from the VCF file. If not supplied the sample name from the BAM read group header is used instead.") public String 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(shortName="IGNORE_RG", doc="If 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