public final class Utils extends Object
| Modifier and Type | Field and Description |
|---|---|
static String |
HEADERMERGER_INPUTS_PROPERTY |
static String |
WORK_FILENAME_PROPERTY |
| Constructor and Description |
|---|
Utils() |
| Modifier and Type | Method and Description |
|---|---|
static void |
configureSampling(org.apache.hadoop.fs.Path workDir,
String outName,
org.apache.hadoop.conf.Configuration conf) |
static void |
correctSAMRecordForMerging(htsjdk.samtools.SAMRecord r,
org.apache.hadoop.conf.Configuration conf)
Changes the given SAMRecord as appropriate for being placed in a file
whose header is getSAMHeaderMerger(conf).getMergedHeader().
|
static String |
getArgv0() |
static org.apache.hadoop.fs.Path |
getMergeableWorkFile(org.apache.hadoop.fs.Path directory,
String basePrefix,
String basePostfix,
org.apache.hadoop.mapreduce.TaskAttemptContext ctx,
String extension)
Returns a name that mergeInto() will recognize as a file to be merged.
|
static htsjdk.samtools.SamFileHeaderMerger |
getSAMHeaderMerger(org.apache.hadoop.conf.Configuration conf)
Computes the merger of the SAM headers in the files listed in
HEADERMERGER_INPUTS_PROPERTY.
|
static String |
getStringencyOptHelp() |
static void |
mergeInto(OutputStream out,
org.apache.hadoop.fs.Path directory,
String basePrefix,
String basePostfix,
org.apache.hadoop.conf.Configuration conf,
String commandName)
Merges the files in the given directory that have names given by
getMergeableWorkFile() into out.
|
static void |
mergeSAMInto(org.apache.hadoop.fs.Path out,
org.apache.hadoop.fs.Path directory,
String basePrefix,
String basePostfix,
SAMFormat format,
org.apache.hadoop.conf.Configuration conf,
String commandName)
Merges the files in the given directory that have names given by
getMergeableWorkFile() into out in the given SAMFormat, using
getSAMHeaderMerger().getMergedHeader() as the header.
|
static void |
printWrapped(PrintStream out,
String str) |
static void |
printWrapped(PrintStream out,
String str,
int indent) |
static void |
printWrapped(PrintStream out,
String str,
int indent,
int wrapAt) |
static void |
setArgv0Class(Class<?> cl) |
static void |
setHeaderMergerSortOrder(org.apache.hadoop.conf.Configuration conf,
htsjdk.samtools.SAMFileHeader.SortOrder order) |
static htsjdk.samtools.ValidationStringency |
toStringency(Object o,
String cmdName)
Sets the default validation stringency in addition to returning it.
|
public static final String WORK_FILENAME_PROPERTY
public static final String HEADERMERGER_INPUTS_PROPERTY
public static void printWrapped(PrintStream out, String str)
public static void printWrapped(PrintStream out, String str, int indent)
public static void printWrapped(PrintStream out, String str, int indent, int wrapAt)
public static String getArgv0()
public static void setArgv0Class(Class<?> cl)
public static void configureSampling(org.apache.hadoop.fs.Path workDir,
String outName,
org.apache.hadoop.conf.Configuration conf)
throws IOException
IOExceptionpublic static org.apache.hadoop.fs.Path getMergeableWorkFile(org.apache.hadoop.fs.Path directory,
String basePrefix,
String basePostfix,
org.apache.hadoop.mapreduce.TaskAttemptContext ctx,
String extension)
public static void mergeInto(OutputStream out, org.apache.hadoop.fs.Path directory, String basePrefix, String basePostfix, org.apache.hadoop.conf.Configuration conf, String commandName) throws IOException
IOExceptionpublic static void setHeaderMergerSortOrder(org.apache.hadoop.conf.Configuration conf,
htsjdk.samtools.SAMFileHeader.SortOrder order)
public static htsjdk.samtools.SamFileHeaderMerger getSAMHeaderMerger(org.apache.hadoop.conf.Configuration conf)
throws IOException
IOExceptionpublic static void correctSAMRecordForMerging(htsjdk.samtools.SAMRecord r,
org.apache.hadoop.conf.Configuration conf)
throws IOException
IOExceptionpublic static void mergeSAMInto(org.apache.hadoop.fs.Path out,
org.apache.hadoop.fs.Path directory,
String basePrefix,
String basePostfix,
SAMFormat format,
org.apache.hadoop.conf.Configuration conf,
String commandName)
throws IOException
IOExceptionpublic static String getStringencyOptHelp()
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