public class FilterSamReads extends CommandLineProgram
Modifier and Type | Field and Description |
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picard.sam.FilterSamReads.Filter |
FILTER |
File |
INPUT |
File |
OUTPUT |
File |
READ_LIST_FILE |
SAMFileHeader.SortOrder |
SORT_ORDER |
boolean |
WRITE_READS_FILES |
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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FilterSamReads() |
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.
|
protected int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(String[] args)
Stock main method.
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getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(doc="The SAM or BAM file that will be filtered.", optional=false, shortName="I") public File INPUT
@Option(doc="Read List File containing reads that will be included or excluded from the OUTPUT SAM or BAM file.", optional=true, shortName="RLF") public File READ_LIST_FILE
@Option(doc="SortOrder of the OUTPUT SAM or BAM file, otherwise use the SortOrder of the INPUT file.", optional=true, shortName="SO") public SAMFileHeader.SortOrder SORT_ORDER
@Option(doc="Create .reads files (for debugging purposes)", optional=true) public boolean WRITE_READS_FILES
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
protected String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram
public static void main(String[] args)
args
- main arguments