public abstract class AbstractVariationFile extends Object
Modifier and Type | Field and Description |
---|---|
protected BufferedReader |
fileReader |
protected org.slf4j.Logger |
logger |
protected String |
preprocessedFileName |
protected String |
unprocessedFileName |
protected Path |
variationDirectory |
protected int |
variationIdColumnIndex |
Constructor and Description |
---|
AbstractVariationFile(Path variationDirectory,
String unprocessedFileName,
String preprocessedFileName) |
AbstractVariationFile(Path variationDirectory,
String unprocessedFileName,
String preprocessedFileName,
int variationIdColumnIndexInFile) |
Modifier and Type | Method and Description |
---|---|
void |
createBufferedReader() |
boolean |
existsZippedOrUnzippedFile() |
protected boolean |
existsZippedOrUnzippedFile(String baseFilename) |
protected BufferedReader |
getBufferedReader(String fileName) |
protected BufferedReader |
getUnprocessedFileBufferedReader() |
List<String[]> |
getVariationRelatedLines(int variationId) |
void |
gunzip() |
void |
gzip() |
boolean |
isEmpty() |
void |
sort() |
protected void |
sortFileByNumericColumn(Path inputFile,
Path outputFile,
int columnIndex) |
protected org.slf4j.Logger logger
protected Path variationDirectory
protected String unprocessedFileName
protected String preprocessedFileName
protected BufferedReader fileReader
protected int variationIdColumnIndex
public AbstractVariationFile(Path variationDirectory, String unprocessedFileName, String preprocessedFileName)
public void createBufferedReader() throws IOException
IOException
protected BufferedReader getBufferedReader(String fileName) throws IOException
IOException
protected BufferedReader getUnprocessedFileBufferedReader() throws IOException
IOException
public List<String[]> getVariationRelatedLines(int variationId) throws IOException
IOException
public void gunzip() throws IOException, InterruptedException
IOException
InterruptedException
protected boolean existsZippedOrUnzippedFile(String baseFilename)
public void sort() throws IOException, InterruptedException
IOException
InterruptedException
protected void sortFileByNumericColumn(Path inputFile, Path outputFile, int columnIndex) throws InterruptedException, IOException
InterruptedException
IOException
public void gzip() throws IOException, InterruptedException
IOException
InterruptedException
public boolean existsZippedOrUnzippedFile()
public boolean isEmpty() throws IOException
IOException
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