public class BEDCodec extends AsciiFeatureCodec<BEDFeature>
Modifier and Type | Class and Description |
---|---|
static class |
BEDCodec.StartOffset
Indicate whether co-ordinates or 0-based or 1-based.
|
Modifier and Type | Field and Description |
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static java.lang.String |
BED_EXTENSION
Deprecated.
since June 2019 Use
FileExtensions.BED instead. |
Constructor and Description |
---|
BEDCodec()
Calls
BEDCodec(StartOffset) with an argument
of StartOffset.ONE |
BEDCodec(BEDCodec.StartOffset startOffset)
BED format is 0-based, but Tribble is 1-based.
|
Modifier and Type | Method and Description |
---|---|
boolean |
canDecode(java.lang.String path)
This function returns true iff the File potentialInput can be parsed by this
codec.
|
BEDFeature |
decode(java.lang.String line) |
BEDFeature |
decode(java.lang.String[] tokens) |
BEDFeature |
decodeLoc(java.lang.String line) |
int |
getStartOffset() |
TabixFormat |
getTabixFormat()
Define the tabix format for the feature, used for indexing.
|
java.lang.Object |
readActualHeader(LineIterator lineIterator)
The BED codec doesn't retain the actual header, but we need to parse through
it and advance to the beginning of the first feature.
|
protected boolean |
readHeaderLine(java.lang.String line) |
close, decode, isDone, makeIndexableSourceFromStream, makeSourceFromStream, readHeader
decodeLoc, getFeatureType
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getPathToDataFile
@Deprecated public static final java.lang.String BED_EXTENSION
FileExtensions.BED
instead.public BEDCodec()
BEDCodec(StartOffset)
with an argument
of StartOffset.ONE
public BEDCodec(BEDCodec.StartOffset startOffset)
public BEDFeature decodeLoc(java.lang.String line)
public BEDFeature decode(java.lang.String line)
decode
in class AsciiFeatureCodec<BEDFeature>
AsciiFeatureCodec.decode(htsjdk.tribble.readers.LineIterator)
public java.lang.Object readActualHeader(LineIterator lineIterator)
readActualHeader
in class AsciiFeatureCodec<BEDFeature>
lineIterator
- public BEDFeature decode(java.lang.String[] tokens)
protected boolean readHeaderLine(java.lang.String line)
public boolean canDecode(java.lang.String path)
FeatureCodec
This function returns true iff the File potentialInput can be parsed by this codec. Note that checking the file's extension is a perfectly acceptable implementation of this method and file contents only rarely need to be checked.
There is an assumption that there's never a situation where two different Codecs return true for the same file. If this occurs, the recommendation would be to error out.
Note this function must never throw an error. All errors should be trapped and false returned.path
- the file to test for parsability with this codecpublic int getStartOffset()
public TabixFormat getTabixFormat()
FeatureCodec
AsciiFeatureCodec
could read tabix files as defined in
AbstractFeatureReader.getFeatureReader(String, String, FeatureCodec, boolean, java.util.function.Function, java.util.function.Function)