CountRecords (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.tribble.example.CountRecords

```
public class CountRecords
extends Object
```
An example of how to index a feature file, and then count all the records in the file. This is also useful for testing the feature reader

Constructor Summary

Constructors
Constructor and Description

CountRecords()

Constructors
Constructor and Description
`CountRecords()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static Index`	`createAndWriteNewIndex(File featureFile, File indexFile, FeatureCodec codec)` creates a new index, given the feature file and the codec
`static FeatureCodec`	`getFeatureCodec(File featureFile)` Return a `FeatureCodec` instance appropriate for the given `featureFile`.
`static Index`	`loadIndex(File featureFile, FeatureCodec codec)`
`static void`	`main(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(File featureInput, FeatureCodec codec, int optimizeThreshold)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - CountRecords
```
public CountRecords()
```
- Method Detail
  - main
```
public static void main(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
    
    Parameters:
    
    args - a single parameter, the file name to load
  - runWithIndex
```
public static long runWithIndex(File featureInput,
                                FeatureCodec codec,
                                int optimizeThreshold)
```
    Parameters:
    
    featureInput - File containing features
    
    codec - Codec used to read the features
    
    optimizeThreshold - Threshold used to optimize the linear index
    
    Returns:
    
    See Also:
    
    LinearIndex.optimize(double)
  - printUsage
```
public static void printUsage()
```
    print usage information
  - loadIndex
```
public static Index loadIndex(File featureFile,
                              FeatureCodec codec)
```
    Parameters:
    
    featureFile - the feature file
    
    codec - the codec to decode features with
    
    Returns:
    
    an index instance
  - createAndWriteNewIndex
```
public static Index createAndWriteNewIndex(File featureFile,
                                           File indexFile,
                                           FeatureCodec codec)
```
    creates a new index, given the feature file and the codec
    
    Parameters:
    
    featureFile - the feature file (i.e. .vcf, .bed)
    
    indexFile - the index file; the location we should be writing the index to
    
    codec - the codec to read features with
    
    Returns:
    
    an index instance
  - getFeatureCodec
```
public static FeatureCodec getFeatureCodec(File featureFile)
```
    Return a FeatureCodec instance appropriate for the given featureFile. Codec is generated based on file extension
    
    Parameters:
    
    featureFile -
    
    Returns:
    
    Throws:
    
    IllegalArgumentException - If a codec cannot be found

Class CountRecords

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

CountRecords

Method Detail

main

runWithIndex

printUsage

loadIndex

createAndWriteNewIndex

getFeatureCodec