public class ViewSam extends CommandLineProgram
Modifier and Type | Class and Description |
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static class |
ViewSam.AlignmentStatus |
static class |
ViewSam.PfStatus |
Modifier and Type | Field and Description |
---|---|
ViewSam.AlignmentStatus |
ALIGNMENT_STATUS |
boolean |
HEADER_ONLY |
java.lang.String |
INPUT |
java.io.File |
INTERVAL_LIST |
ViewSam.PfStatus |
PF_STATUS |
boolean |
RECORDS_ONLY |
java.lang.String |
USAGE |
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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ViewSam() |
Modifier and Type | Method and Description |
---|---|
protected java.lang.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(java.lang.String[] args) |
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
public final java.lang.String USAGE
@Option(shortName="I", doc="The SAM or BAM file or GA4GH url to view.") public java.lang.String INPUT
@Option(doc="Print out all reads, just the aligned reads or just the unaligned reads.") public ViewSam.AlignmentStatus ALIGNMENT_STATUS
@Option(doc="Print out all reads, just the PF reads or just the non-PF reads.") public ViewSam.PfStatus PF_STATUS
@Option(doc="Print the alignment records only.", optional=true) public boolean RECORDS_ONLY
public static void main(java.lang.String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
protected java.lang.String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram