Field Detail

• HTSGET_SCHEME

  public static final String HTSGET_SCHEME

  See Also:

  Constant Field Values

Constructor Detail

• HtsgetBAMFileReader

  public HtsgetBAMFileReader​(URI source,
                             boolean eagerDecode,
                             ValidationStringency validationStringency,
                             SAMRecordFactory samRecordFactory,
                             boolean useAsynchronousIO)
                      throws 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:

  IOException

• HtsgetBAMFileReader

  public HtsgetBAMFileReader​(URI source,
                             boolean eagerDecode,
                             ValidationStringency validationStringency,
                             SAMRecordFactory samRecordFactory,
                             boolean useAsynchronousIO,
                             InflaterFactory inflaterFactory)
                      throws 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:

  IOException

Method Detail

• fromHtsgetURI

  public static HtsgetBAMFileReader fromHtsgetURI​(htsjdk.samtools.HtsgetInputResource source,
                                                  boolean eagerDecode,
                                                  ValidationStringency validationStringency,
                                                  SAMRecordFactory samRecordFactory,
                                                  boolean useAsynchronousIO,
                                                  InflaterFactory inflaterFactory)
                                           throws IOException,
                                                  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:

  IOException

  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()

• 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​(String sequence,
                                            int start,
                                            int end,
                                            boolean contained)

• query

  public CloseableIterator<SAMRecord> query​(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​(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 URI convertHtsgetUriToHttps​(URI uri)
                                     throws URISyntaxException

  Throws:

  URISyntaxException

• convertHtsgetUriToHttp

  public static URI convertHtsgetUriToHttp​(URI uri)
                                    throws URISyntaxException

  Throws:

  URISyntaxException