htsjdk.samtools

Class HtsgetBAMFileReader

java.lang.Object

htsjdk.samtools.SamReader.ReaderImplementation

htsjdk.samtools.HtsgetBAMFileReader

All Implemented Interfaces:

SamReader.PrimitiveSamReader

public class HtsgetBAMFileReader
extends SamReader.ReaderImplementation

Class for reading and querying BAM files from an htsget source

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter Filters out records that do not match any of the given intervals and query type.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	HTSGET_SCHEME

Constructor Summary

Constructors

Constructor and Description
HtsgetBAMFileReader(java.net.URI source, boolean eagerDecode, ValidationStringency validationStringency, SAMRecordFactory samRecordFactory, boolean useAsynchronousIO) Prepare to read BAM from an htsget source
HtsgetBAMFileReader(java.net.URI source, boolean eagerDecode, ValidationStringency validationStringency, SAMRecordFactory samRecordFactory, boolean useAsynchronousIO, InflaterFactory inflaterFactory) Prepare to read BAM from a htsget source

Method Summary

Modifier and Type	Method and Description
void	close()
static java.net.URI	convertHtsgetUriToHttp(java.net.URI uri)
static java.net.URI	convertHtsgetUriToHttps(java.net.URI uri)
void	enableCrcChecking(boolean check) Set whether to check CRC for subsequent iterator or query requests.
void	enableFileSource(SamReader reader, boolean enabled) Set whether to write the source of every read into the source SAMRecords.
static HtsgetBAMFileReader	fromHtsgetURI(htsjdk.samtools.HtsgetInputResource source, boolean eagerDecode, ValidationStringency validationStringency, SAMRecordFactory samRecordFactory, boolean useAsynchronousIO, InflaterFactory inflaterFactory) Instantiate an HtsgetBAMFileReader from an HtsgetInputResource, attempting to convert it to an https resource then a http resource if the server does not support https
SAMFileHeader	getFileHeader()
SAMFileSpan	getFilePointerSpanningReads() Generally gets a pointer to the first read in the file.
BAMIndex	getIndex() Always null as htsget sources do not have indices
CloseableIterator<SAMRecord>	getIterator() Prepare to iterate through the SAMRecords in file order.
CloseableIterator<SAMRecord>	getIterator(SAMFileSpan fileSpan) Generally loads data at a given point in the file.
ValidationStringency	getValidationStringency()
boolean	hasIndex() Always false as htsget sources do not have indices
boolean	isQueryable() Note that this source is queryable by interval despite NOT having an index
boolean	isUsingPOST() Can be used to determine whether the specified source supports the POST api
CloseableIterator<SAMRecord>	query(java.util.List<Locatable> intervals, boolean contained) Query intervals directly by contig name instead of index relative to reference, to avoid repeated conversion between name and index representations
CloseableIterator<SAMRecord>	query(QueryInterval[] intervals, boolean contained) Prepare to iterate through the SAMRecords that match the given interval.
CloseableIterator<SAMRecord>	query(java.lang.String sequence, int start, int end, boolean contained)
CloseableIterator<SAMRecord>	queryAlignmentStart(java.lang.String sequence, int start) Prepare to iterate through the SAMRecords with the given alignment start.
CloseableIterator<SAMRecord>	queryUnmapped() Prepare to iterate through the SAMRecords that are unmapped and do not have a reference name or alignment start.
void	setEagerDecode(boolean eagerDecode) Set whether to eagerly decode subsequent SAMRecord reads.
void	setSAMRecordFactory(SAMRecordFactory samRecordFactory) Set SAMRecordFactory for subsequent SAMRecord reads.
void	setUsingPOST(boolean use) Force the source to attempt to use the POST api when requesting multiple intervals.
void	setValidationStringency(ValidationStringency validationStringency) Set error-checking level for subsequent SAMRecord reads.
SamReader.Type	type()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

HTSGET_SCHEME

public static final java.lang.String HTSGET_SCHEME

See Also:

Constant Field Values

Constructor Detail

HtsgetBAMFileReader

public HtsgetBAMFileReader(java.net.URI source,
                           boolean eagerDecode,
                           ValidationStringency validationStringency,
                           SAMRecordFactory samRecordFactory,
                           boolean useAsynchronousIO)
                    throws java.io.IOException

Prepare to read BAM from an htsget source

Parameters:

source - http(s) URI of htsget resource including ID

eagerDecode - if true, decode all BAM fields as reading rather than lazily.

validationStringency - Controls how to handle invalidate reads or header lines.

samRecordFactory - SAM record factory

useAsynchronousIO - if true, use asynchronous I/O and prefetching

Throws:

java.io.IOException

HtsgetBAMFileReader

public HtsgetBAMFileReader(java.net.URI source,
                           boolean eagerDecode,
                           ValidationStringency validationStringency,
                           SAMRecordFactory samRecordFactory,
                           boolean useAsynchronousIO,
                           InflaterFactory inflaterFactory)
                    throws java.io.IOException

Prepare to read BAM from a htsget source

Parameters:

source - source of bytes.

eagerDecode - if true, decode all BAM fields as reading rather than lazily.

validationStringency - Controls how to handle invalidate reads or header lines.

samRecordFactory - SAM record factory

useAsynchronousIO - if true, use asynchronous I/O and prefetching

inflaterFactory - InflaterFactory used by BlockCompressedInputStream

Throws:

java.io.IOException

Method Detail

fromHtsgetURI

public static HtsgetBAMFileReader fromHtsgetURI(htsjdk.samtools.HtsgetInputResource source,
                                                boolean eagerDecode,
                                                ValidationStringency validationStringency,
                                                SAMRecordFactory samRecordFactory,
                                                boolean useAsynchronousIO,
                                                InflaterFactory inflaterFactory)
                                         throws java.io.IOException,
                                                java.net.URISyntaxException

Instantiate an HtsgetBAMFileReader from an HtsgetInputResource, attempting to convert it to an https resource then a http resource if the server does not support https

Parameters:

source - source of bytes.

eagerDecode - if true, decode all BAM fields as reading rather than lazily.

validationStringency - Controls how to handle invalidate reads or header lines.

samRecordFactory - SAM record factory

useAsynchronousIO - if true, use asynchronous I/O and prefetching

inflaterFactory - InflaterFactory used by BlockCompressedInputStream

Throws:

java.io.IOException

java.net.URISyntaxException

setValidationStringency

public void setValidationStringency(ValidationStringency validationStringency)

Set error-checking level for subsequent SAMRecord reads.

setSAMRecordFactory

public void setSAMRecordFactory(SAMRecordFactory samRecordFactory)

Set SAMRecordFactory for subsequent SAMRecord reads.

setEagerDecode

public void setEagerDecode(boolean eagerDecode)

Set whether to eagerly decode subsequent SAMRecord reads.

enableCrcChecking

public void enableCrcChecking(boolean check)

Set whether to check CRC for subsequent iterator or query requests.

enableFileSource

public void enableFileSource(SamReader reader,
                             boolean enabled)

Set whether to write the source of every read into the source SAMRecords.

type

public SamReader.Type type()

isQueryable

public boolean isQueryable()

Note that this source is queryable by interval despite NOT having an index

Returns:

true

hasIndex

public boolean hasIndex()

Always false as htsget sources do not have indices

Returns:

false

getIndex

public BAMIndex getIndex()

Always null as htsget sources do not have indices

Returns:

null

getFileHeader

public SAMFileHeader getFileHeader()

isUsingPOST

public boolean isUsingPOST()

Can be used to determine whether the specified source supports the POST api

setUsingPOST

public void setUsingPOST(boolean use)

Force the source to attempt to use the POST api when requesting multiple intervals. Used for testing

Parameters:

use - whether to use the POST api

getIterator

public CloseableIterator<SAMRecord> getIterator()

Prepare to iterate through the SAMRecords in file order. Unlike file-based BAM readers, multiple iterators may be open at the same time

getIterator

public CloseableIterator<SAMRecord> getIterator(SAMFileSpan fileSpan)

Generally loads data at a given point in the file. Unsupported for HtsgetBAMFileReaders.

Parameters:

fileSpan - The file span.

Returns:

An iterator over the given file span.

getFilePointerSpanningReads

public SAMFileSpan getFilePointerSpanningReads()

Generally gets a pointer to the first read in the file. Unsupported for HtsgetBAMFileReaders.

Returns:

An pointer to the first read in the file.

query

public CloseableIterator<SAMRecord> query(QueryInterval[] intervals,
                                          boolean contained)

Prepare to iterate through the SAMRecords that match the given interval. Unlike file-based BAM readers, multiple iterators may be open at the same time

Note that an unmapped SAMRecord may still have a reference name and an alignment start for sorting purposes (typically this is the coordinate of its mate), and will be found by this method if the coordinate matches the specified interval.

Parameters:

intervals - the intervals to include

contained - If true, the alignments for the SAMRecords must be completely contained in the interval specified by start and end. If false, the SAMRecords need only overlap the interval.

Returns:

Iterator for the matching SAMRecords

query

public CloseableIterator<SAMRecord> query(java.lang.String sequence,
                                          int start,
                                          int end,
                                          boolean contained)

query

public CloseableIterator<SAMRecord> query(java.util.List<Locatable> intervals,
                                          boolean contained)

Query intervals directly by contig name instead of index relative to reference, to avoid repeated conversion between name and index representations

Callers much ensure that the intervals are in increasing order and do not overlap or abut

Parameters:

intervals - intervals to query by

contained - only return reads that are fully contained and not just overlapping if this is true

queryAlignmentStart

public CloseableIterator<SAMRecord> queryAlignmentStart(java.lang.String sequence,
                                                        int start)

Prepare to iterate through the SAMRecords with the given alignment start. Unlike file-based BAM readers, multiple iterators may be open at the same time

Note that an unmapped SAMRecord may still have a reference name and an alignment start for sorting purposes (typically this is the coordinate of its mate), and will be found by this method if the coordinate matches the specified interval.

Parameters:

sequence - Reference sequence sought.

start - Alignment start sought.

Returns:

Iterator for the matching SAMRecords.

queryUnmapped

public CloseableIterator<SAMRecord> queryUnmapped()

Prepare to iterate through the SAMRecords that are unmapped and do not have a reference name or alignment start. Unlike file-based BAM readers, multiple iterators may be open at the same time

Returns:

Iterator for the matching SAMRecords.

close

public void close()

getValidationStringency

public ValidationStringency getValidationStringency()

convertHtsgetUriToHttps

public static java.net.URI convertHtsgetUriToHttps(java.net.URI uri)
                                            throws java.net.URISyntaxException

Throws:

java.net.URISyntaxException

convertHtsgetUriToHttp

public static java.net.URI convertHtsgetUriToHttp(java.net.URI uri)
                                           throws java.net.URISyntaxException

Throws:

java.net.URISyntaxException