public class CompareSAMs extends CommandLineProgram
Modifier and Type | Field | Description |
---|---|---|
List<File> |
samFiles |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor | Description |
---|---|
CompareSAMs() |
Modifier and Type | Method | Description |
---|---|---|
boolean |
areEqual() |
|
protected int |
doWork() |
Do the work after command line has been parsed.
|
int |
getMappingsDiffer() |
|
int |
getMappingsMatch() |
|
int |
getMissingLeft() |
|
int |
getMissingRight() |
|
int |
getUnmappedBoth() |
|
int |
getUnmappedLeft() |
|
int |
getUnmappedRight() |
|
static void |
main(String[] argv) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@PositionalArguments(minElements=2, maxElements=2) public List<File> samFiles
public static void main(String[] argv)
protected int doWork()
doWork
in class CommandLineProgram
public int getMappingsMatch()
public int getUnmappedBoth()
public int getUnmappedLeft()
public int getUnmappedRight()
public int getMappingsDiffer()
public int getMissingLeft()
public int getMissingRight()
public boolean areEqual()