Package picard.sam
Class ReplaceSamHeader
- java.lang.Object
-
- picard.cmdline.CommandLineProgram
-
- picard.sam.ReplaceSamHeader
-
@DocumentedFeature public class ReplaceSamHeader extends CommandLineProgram
-
-
Field Summary
Fields Modifier and Type Field Description File
HEADER
File
INPUT
File
OUTPUT
-
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, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
-
-
Constructor Summary
Constructors Constructor Description ReplaceSamHeader()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
-
-
-
-
Field Detail
-
INPUT
@Argument(doc="SAM file from which SAMRecords will be read.", shortName="I") public File INPUT
-
HEADER
@Argument(doc="SAM file from which SAMFileHeader will be read.") public File HEADER
-
OUTPUT
@Argument(doc="SAMFileHeader from HEADER file will be written to this file, followed by SAMRecords from INPUT file", shortName="O") public File OUTPUT
-
-
Method Detail
-
doWork
protected int doWork()
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.
-
-