Interface | Description |
---|---|
htsjdk.samtools.util.Lazy.LazyInitializer |
since 1/2017 use a
Supplier instead |
Class | Description |
---|---|
htsjdk.samtools.filter.FilteringIterator |
use
FilteringSamIterator instead |
htsjdk.samtools.filter.NotPrimaryAlignmentFilter |
use
SecondaryAlignmentFilter instead. |
htsjdk.samtools.FixBAMFile |
since 07/2017. This tool is undocumented and untested.
|
htsjdk.samtools.NotPrimarySkippingIterator |
use
SecondaryAlignmentSkippingIterator instead. |
htsjdk.samtools.SAMTools |
since 07/2017. This class does not add anything to the HTSJDK library except an example of how to iterate over a SAM/BAM file.
In addition, it is not tested.
|
htsjdk.samtools.util.CollectionUtil.Partitioner |
use Collectors.groupingBy instead
|
htsjdk.samtools.util.StringLineReader | |
htsjdk.variant.variantcontext.filter.FilteringIterator |
since 2/29/16 use
FilteringVariantContextIterator instead |
htsjdk.variant.variantcontext.writer.SortingVariantContextWriter |
9/2017, this class is completely untested and unsupported, there is no replacement at this time
if you use this class please file an issue on github or it will be removed at some point in the future
|
Field | Description |
---|---|
htsjdk.samtools.util.IOUtil.STANDARD_BUFFER_SIZE |
Use
Defaults.NON_ZERO_BUFFER_SIZE instead. |
htsjdk.variant.vcf.VCFConstants.GENOTYPE_LIKELIHOODS_KEY |
Constructor | Description |
---|---|
htsjdk.samtools.CRAMIterator(SeekableStream, CRAMReferenceSource, long[]) | |
htsjdk.samtools.MergingSamRecordIterator(SamFileHeaderMerger, boolean) | |
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder) | |
htsjdk.samtools.SAMSequenceRecord(String) |
Use
SAMSequenceRecord(String, int) instead.
sequenceLength is required for the object to be considered valid. |
htsjdk.tribble.readers.AsciiLineReader(InputStream) |
8/8/2017 use
AsciiLineReader.from(java.io.InputStream) |
Enum Constant | Description |
---|---|
htsjdk.samtools.SAMFlag.NOT_PRIMARY_ALIGNMENT |
use
SAMFlag.SECONDARY_ALIGNMENT instead. |