Interface and Description |
---|
htsjdk.samtools.util.Lazy.LazyInitializer
since 1/2017 use a
Supplier instead |
Class and Description |
---|
htsjdk.samtools.util.CollectionUtil.Partitioner
use Collectors.groupingBy instead
|
htsjdk.samtools.filter.FilteringIterator
use
FilteringSamIterator instead |
htsjdk.variant.variantcontext.filter.FilteringIterator
since 2/29/16 use
FilteringVariantContextIterator instead |
htsjdk.samtools.FixBAMFile
since 07/2017. This tool is undocumented and untested.
|
htsjdk.samtools.filter.NotPrimaryAlignmentFilter
use
SecondaryAlignmentFilter instead. |
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.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
|
htsjdk.samtools.util.StringLineReader |
Field and Description |
---|
htsjdk.variant.vcf.VCFConstants.GENOTYPE_LIKELIHOODS_KEY |
htsjdk.samtools.util.IOUtil.STANDARD_BUFFER_SIZE
Use
Defaults.NON_ZERO_BUFFER_SIZE instead. |
Constructor and Description |
---|
htsjdk.tribble.readers.AsciiLineReader(InputStream)
8/8/2017 use
AsciiLineReader.from(java.io.InputStream) |
htsjdk.tribble.readers.AsciiLineReader(PositionalBufferedStream)
8/8/2017 use
AsciiLineReader.from(java.io.InputStream) |
htsjdk.samtools.CRAMIterator(SeekableStream, CRAMReferenceSource, long[]) |
htsjdk.samtools.MergingSamRecordIterator(SamFileHeaderMerger, boolean) |
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder) |
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder, boolean) |
htsjdk.samtools.SAMSequenceRecord(String)
Use
SAMSequenceRecord.SAMSequenceRecord(String, int) instead.
sequenceLength is required for the object to be considered valid. |
Enum Constant and Description |
---|
htsjdk.samtools.SAMFlag.NOT_PRIMARY_ALIGNMENT
use
SAMFlag.SECONDARY_ALIGNMENT instead. |