public class CountRecords
extends java.lang.Object
| Constructor and Description |
|---|
CountRecords() |
| Modifier and Type | Method and Description |
|---|---|
static Index |
createAndWriteNewIndex(java.io.File featureFile,
java.io.File indexFile,
FeatureCodec codec)
creates a new index, given the feature file and the codec
|
static FeatureCodec |
getFeatureCodec(java.io.File featureFile)
Return a
FeatureCodec instance appropriate for the given
featureFile. |
static Index |
loadIndex(java.io.File featureFile,
FeatureCodec codec) |
static void |
main(java.lang.String[] args)
The main method of this class:
1) checks to see that the feature file exists
2) loads an index from disk, if one doesn't exist, it creates it and writes it to disk
3) creates a FeatureSource
4) iterates over the records, emitting a final tally for the number of features seen
|
static void |
printUsage()
print usage information
|
static long |
runWithIndex(java.io.File featureInput,
FeatureCodec codec,
int optimizeThreshold) |
public static void main(java.lang.String[] args)
args - a single parameter, the file name to loadpublic static long runWithIndex(java.io.File featureInput,
FeatureCodec codec,
int optimizeThreshold)
featureInput - File containing featurescodec - Codec used to read the featuresoptimizeThreshold - Threshold used to optimize the linear indexLinearIndex.optimize(double)public static void printUsage()
public static Index loadIndex(java.io.File featureFile, FeatureCodec codec)
featureFile - the feature filecodec - the codec to decode features withpublic static Index createAndWriteNewIndex(java.io.File featureFile, java.io.File indexFile, FeatureCodec codec)
featureFile - the feature file (i.e. .vcf, .bed)indexFile - the index file; the location we should be writing the index tocodec - the codec to read features withpublic static FeatureCodec getFeatureCodec(java.io.File featureFile)
FeatureCodec instance appropriate for the given
featureFile. Codec is generated based on file extensionfeatureFile - java.lang.IllegalArgumentException - If a codec cannot be found