public class MergeSamFiles extends CommandLineProgram
Modifier and Type | Field and Description |
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boolean |
ASSUME_SORTED |
List<String> |
COMMENT |
List<File> |
INPUT |
boolean |
MERGE_SEQUENCE_DICTIONARIES |
File |
OUTPUT |
SAMFileHeader.SortOrder |
SORT_ORDER |
boolean |
USE_THREADING |
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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MergeSamFiles() |
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()
Combines multiple SAM/BAM files into one.
|
static void |
main(String[] argv)
Required main method implementation.
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getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="SO", doc="Sort order of output file", optional=true) public SAMFileHeader.SortOrder SORT_ORDER
@Option(doc="If true, assume that the input files are in the same sort order as the requested output sort order, even if their headers say otherwise.", shortName="AS") public boolean ASSUME_SORTED
@Option(shortName="MSD", doc="Merge the sequence dictionaries", optional=true) public boolean MERGE_SEQUENCE_DICTIONARIES
@Option(doc="Option to create a background thread to encode, compress and write to disk the output file. The threaded version uses about 20% more CPU and decreases runtime by ~20% when writing out a compressed BAM file.") public boolean USE_THREADING
public static void main(String[] argv)
protected int doWork()
doWork
in class CommandLineProgram
protected String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram