Package picard.vcf
Class VcfFormatConverter
java.lang.Object
picard.cmdline.CommandLineProgram
picard.vcf.VcfFormatConverter
Converts an ASCII VCF file to a binary BCF or vice versa.
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final htsjdk.samtools.util.Log
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected int
doWork()
Do the work after command line has been parsed.Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
-
Field Details
-
LOG
public static final htsjdk.samtools.util.Log LOG -
INPUT
-
OUTPUT
-
REQUIRE_INDEX
@Argument(doc="Fail if an index is not available for the input VCF/BCF") public Boolean REQUIRE_INDEX
-
-
Constructor Details
-
VcfFormatConverter
public VcfFormatConverter()
-
-
Method Details
-
doWork
protected int doWork()Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
-