Package | Description |
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htsjdk.samtools | |
htsjdk.samtools.util |
Modifier and Type | Method and Description |
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static void |
BAMIndexer.createIndex(SamReader reader,
File output,
Log log)
Generates a BAM index file from an input BAM file
|
static void |
CRAMIndexer.createIndex(SeekableStream stream,
File output,
Log log,
ValidationStringency validationStringency)
Generates a BAI index file from an input CRAM stream
|
Modifier and Type | Method and Description |
---|---|
static Log |
Log.getInstance(Class<?> clazz)
Get a Log instance to perform logging within the Class specified.
|
Constructor and Description |
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ProgressLogger(Log log)
Construct a progress logger with the desired log, the verb "Processed" and a period of 1m records.
|
ProgressLogger(Log log,
int n)
Construct a progress logger with the desired log and frequency and the verb "Processed".
|
ProgressLogger(Log log,
int n,
String verb)
Construct a progress logger.
|
ProgressLogger(Log log,
int n,
String verb,
String noun)
Construct a progress logger.
|