@Deprecated public class SAMFileReader extends java.lang.Object implements SamReader, SamReader.Indexing
SamReaderFactory
SamReader.AssertingIterator, SamReader.Indexing, SamReader.PrimitiveSamReader, SamReader.PrimitiveSamReaderToSamReaderAdapter, SamReader.ReaderImplementation, SamReader.Type
Constructor and Description |
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SAMFileReader(java.io.File file)
Deprecated.
Prepare to read a SAM or BAM file.
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SAMFileReader(java.io.File file,
boolean eagerDecode)
Deprecated.
Read a SAM or BAM file, possibly with an index file if present.
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SAMFileReader(java.io.File file,
java.io.File indexFile)
Deprecated.
Prepare to read a SAM or BAM file.
|
SAMFileReader(java.io.File file,
java.io.File indexFile,
boolean eagerDecode)
Deprecated.
Read a SAM or BAM file, possibly with an index file.
|
SAMFileReader(java.io.InputStream stream)
Deprecated.
Prepare to read a SAM or BAM file.
|
SAMFileReader(java.io.InputStream stream,
boolean eagerDecode)
Deprecated.
Read a SAM or BAM file.
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SAMFileReader(SeekableStream strm,
java.io.File indexFile,
boolean eagerDecode)
Deprecated.
Read a BAM file via caller-supplied mechanism.
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SAMFileReader(SeekableStream strm,
SeekableStream indexStream,
boolean eagerDecode)
Deprecated.
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SAMFileReader(java.net.URL url,
java.io.File indexFile,
boolean eagerDecode)
Deprecated.
Read a BAM file by http
indexed query will be allowed.
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Modifier and Type | Method and Description |
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void |
close()
Deprecated.
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void |
enableCrcChecking(boolean enabled)
Deprecated.
Only meaningful for BAM file readers - enables or disables checking of checksums on uncompressed
data during decompression.
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void |
enableFileSource(boolean enabled)
Deprecated.
If true, writes the source of every read into the source SAMRecords.
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void |
enableIndexCaching(boolean enabled)
Deprecated.
If true, uses the caching version of the index reader.
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void |
enableIndexMemoryMapping(boolean enabled)
Deprecated.
If false, disable the use of memory mapping for accessing index files (default behavior is to use memory mapping).
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BrowseableBAMIndex |
getBrowseableIndex()
Deprecated.
Gets an index tagged with the BrowseableBAMIndex interface.
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static ValidationStringency |
getDefaultValidationStringency()
Deprecated.
|
SAMFileHeader |
getFileHeader()
Deprecated.
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SAMFileSpan |
getFilePointerSpanningReads()
Deprecated.
Gets a pointer spanning all reads in the BAM file.
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BAMIndex |
getIndex()
Deprecated.
Retrieves the index for the given file type.
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java.lang.String |
getResourceDescription()
Deprecated.
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static SAMSequenceDictionary |
getSequenceDictionary(java.io.File dictionaryFile)
Deprecated.
Returns the SAMSequenceDictionary from the provided FASTA.
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boolean |
hasBrowseableIndex()
Deprecated.
Returns true if the supported index is browseable, meaning the bins in it can be traversed
and chunk data inspected and retrieved.
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boolean |
hasIndex()
Deprecated.
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SamReader.Indexing |
indexing()
Deprecated.
Exposes the
SamReader.Indexing facet of this SamReader . |
boolean |
isBinary()
Deprecated.
|
SAMRecordIterator |
iterator()
Deprecated.
Iterate through file in order.
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SAMRecordIterator |
iterator(SAMFileSpan chunks)
Deprecated.
Iterate through the given chunks in the file.
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QueryInterval |
makeQueryInterval(java.lang.String sequence,
int start)
Deprecated.
Convenience method to create a QueryInterval that goes from start to end of given sequence.
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QueryInterval |
makeQueryInterval(java.lang.String sequence,
int start,
int end)
Deprecated.
Convenience method to create a QueryInterval
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SAMRecordIterator |
query(QueryInterval[] intervals,
boolean contained)
Deprecated.
Iterate over records that match one of the given intervals.
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SAMRecordIterator |
query(java.lang.String sequence,
int start,
int end,
boolean contained)
Deprecated.
Iterate over records that match the given interval.
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SAMRecordIterator |
queryAlignmentStart(java.lang.String sequence,
int start)
Deprecated.
Iterate over records that map to the given sequence and start at the given position.
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SAMRecordIterator |
queryContained(QueryInterval[] intervals)
Deprecated.
Iterate over records that are contained in the given interval.
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SAMRecordIterator |
queryContained(java.lang.String sequence,
int start,
int end)
Deprecated.
Iterate over records that are contained in the given interval.
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SAMRecord |
queryMate(SAMRecord rec)
Deprecated.
Fetch the mate for the given read.
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SAMRecordIterator |
queryOverlapping(QueryInterval[] intervals)
Deprecated.
Iterate over records that overlap any of the given intervals.
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SAMRecordIterator |
queryOverlapping(java.lang.String sequence,
int start,
int end)
Deprecated.
Iterate over records that overlap the given interval.
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SAMRecordIterator |
queryUnmapped()
Deprecated.
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static void |
setDefaultValidationStringency(ValidationStringency defaultValidationStringency)
Deprecated.
Set validation stringency for all subsequently-created SAMFileReaders.
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void |
setSAMRecordFactory(SAMRecordFactory factory)
Deprecated.
Override the default SAMRecordFactory class used to instantiate instances of SAMRecord and BAMRecord.
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void |
setValidationStringency(ValidationStringency validationStringency)
Deprecated.
Control validation of SAMRecords as they are read from file.
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java.lang.String |
toString()
Deprecated.
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SamReader.Type |
type()
Deprecated.
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public SAMFileReader(java.io.InputStream stream)
public SAMFileReader(java.io.File file)
public SAMFileReader(java.io.File file, java.io.File indexFile)
file
- SAM or BAM to read.indexFile
- Index file that is companion to BAM, or null if no index file, or if index file
should be found automatically.public SAMFileReader(java.io.InputStream stream, boolean eagerDecode)
stream
- input SAM or BAM. This is buffered internally so caller need not buffer.eagerDecode
- if true, decode SAM record entirely when reading it.public SAMFileReader(java.io.File file, boolean eagerDecode)
file
- SAM or BAM.eagerDecode
- if true, decode SAM record entirely when reading it.public SAMFileReader(java.io.File file, java.io.File indexFile, boolean eagerDecode)
file
- SAM or BAM.indexFile
- Location of index file, or null in order to use the default index file (if present).eagerDecode
- eagerDecode if true, decode SAM record entirely when reading it.public SAMFileReader(java.net.URL url, java.io.File indexFile, boolean eagerDecode)
url
- BAM.indexFile
- Location of index file, or null if indexed access not required.eagerDecode
- eagerDecode if true, decode SAM record entirely when reading it.public SAMFileReader(SeekableStream strm, java.io.File indexFile, boolean eagerDecode)
strm
- BAM -- If the stream is not buffered, caller should wrap in SeekableBufferedStream for
better performance.indexFile
- Location of index file, or null indexed access not required.eagerDecode
- if true, decode SAM record entirely when reading it.public SAMFileReader(SeekableStream strm, SeekableStream indexStream, boolean eagerDecode)
strm
- BAM -- If the stream is not buffered, caller should wrap in SeekableBufferedStream for
better performance.public static ValidationStringency getDefaultValidationStringency()
public static void setDefaultValidationStringency(ValidationStringency defaultValidationStringency)
public static SAMSequenceDictionary getSequenceDictionary(java.io.File dictionaryFile)
public void close()
close
in interface java.io.Closeable
close
in interface java.lang.AutoCloseable
public void enableFileSource(boolean enabled)
enabled
- true to write source information into each SAMRecord.public void enableIndexCaching(boolean enabled)
enabled
- true to write source information into each SAMRecord.public void enableIndexMemoryMapping(boolean enabled)
enabled
- True to use memory mapping, false to use regular I/O.public void enableCrcChecking(boolean enabled)
public void setSAMRecordFactory(SAMRecordFactory factory)
public boolean isBinary()
public boolean hasIndex()
public SamReader.Indexing indexing()
SamReader
SamReader.Indexing
facet of this SamReader
.public BAMIndex getIndex()
getIndex
in interface SamReader.Indexing
public boolean hasBrowseableIndex()
hasBrowseableIndex
in interface SamReader.Indexing
public BrowseableBAMIndex getBrowseableIndex()
getBrowseableIndex
in interface SamReader.Indexing
SAMException
- if no such index is available.public SAMFileHeader getFileHeader()
getFileHeader
in interface SamReader
public SamReader.Type type()
type
in interface SamReader
SamReader.Type
of this SamReader
public java.lang.String getResourceDescription()
getResourceDescription
in interface SamReader
public void setValidationStringency(ValidationStringency validationStringency)
public SAMRecordIterator iterator()
public SAMRecordIterator iterator(SAMFileSpan chunks)
iterator
in interface SamReader.Indexing
chunks
- List of chunks for which to retrieve data.public SAMFileSpan getFilePointerSpanningReads()
getFilePointerSpanningReads
in interface SamReader.Indexing
public SAMRecordIterator query(java.lang.String sequence, int start, int end, boolean contained)
query
in interface SamReader
sequence
- Reference sequence of interest.start
- 1-based, inclusive start of interval of interest. Zero implies start of the reference sequence.end
- 1-based, inclusive end of interval of interest. Zero implies end of the reference sequence.contained
- If true, each SAMRecord returned is will have its alignment completely contained in the
interval of interest. If false, the alignment of the returned SAMRecords need only overlap the interval of interest.public SAMRecordIterator queryOverlapping(java.lang.String sequence, int start, int end)
queryOverlapping
in interface SamReader
sequence
- Reference sequence of interest.start
- 1-based, inclusive start of interval of interest. Zero implies start of the reference sequence.end
- 1-based, inclusive end of interval of interest. Zero implies end of the reference sequence.public SAMRecordIterator queryContained(java.lang.String sequence, int start, int end)
queryContained
in interface SamReader
sequence
- Reference sequence of interest.start
- 1-based, inclusive start of interval of interest. Zero implies start of the reference sequence.end
- 1-based, inclusive end of interval of interest. Zero implies end of the reference sequence.public SAMRecordIterator query(QueryInterval[] intervals, boolean contained)
query
in interface SamReader
intervals
- Intervals to be queried. The intervals must be optimized, i.e. in order, with overlapping
and abutting intervals merged. This can be done with QueryInterval.optimizeIntervals(htsjdk.samtools.QueryInterval[])
contained
- If true, each SAMRecord returned is will have its alignment completely contained in one of the
intervals of interest. If false, the alignment of the returned SAMRecords need only overlap one of
the intervals of interest.public SAMRecordIterator queryOverlapping(QueryInterval[] intervals)
queryOverlapping
in interface SamReader
intervals
- Intervals to be queried. The intervals must be optimized, i.e. in order, with overlapping
and abutting intervals merged. This can be done with QueryInterval.optimizeIntervals(htsjdk.samtools.QueryInterval[])
public SAMRecordIterator queryContained(QueryInterval[] intervals)
queryContained
in interface SamReader
intervals
- Intervals to be queried. The intervals must be optimized, i.e. in order, with overlapping
and abutting intervals merged. This can be done with QueryInterval.optimizeIntervals(htsjdk.samtools.QueryInterval[])
public SAMRecordIterator queryUnmapped()
queryUnmapped
in interface SamReader
public SAMRecordIterator queryAlignmentStart(java.lang.String sequence, int start)
queryAlignmentStart
in interface SamReader
sequence
- Reference sequence of interest.start
- Alignment start of interest.public SAMRecord queryMate(SAMRecord rec)
public java.lang.String toString()
toString
in class java.lang.Object
public QueryInterval makeQueryInterval(java.lang.String sequence, int start, int end)
sequence
- sequence of interest, must exist in sequence dictionarystart
- 1-based start position, must be >= 1end
- 1-based end position.java.lang.IllegalArgumentException
- if sequence not found in sequence dictionary, or start position < 1public QueryInterval makeQueryInterval(java.lang.String sequence, int start)
sequence
- sequence of interest, must exist in sequence dictionarystart
- 1-based start position, must be >= 1java.lang.IllegalArgumentException
- if sequence not found in sequence dictionary, or start position < 1