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Interfaces Interface Description htsjdk.samtools.util.Lazy.LazyInitializer since 1/2017 use aSupplier
instead
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Classes Class Description htsjdk.samtools.filter.FilteringIterator useFilteringSamIterator
insteadhtsjdk.samtools.filter.NotPrimaryAlignmentFilter useSecondaryAlignmentFilter
instead.htsjdk.samtools.FixBAMFile since 07/2017. This tool is undocumented and untested.htsjdk.samtools.NotPrimarySkippingIterator useSecondaryAlignmentSkippingIterator
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 insteadhtsjdk.samtools.util.StringLineReader htsjdk.variant.variantcontext.filter.FilteringIterator since 2/29/16 useFilteringVariantContextIterator
insteadhtsjdk.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
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Constructors Constructor Description htsjdk.samtools.CRAMIterator(SeekableStream, CRAMReferenceSource, long[]) htsjdk.samtools.MergingSamRecordIterator(SamFileHeaderMerger, boolean) htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder) htsjdk.samtools.SAMSequenceRecord(String) UseSAMSequenceRecord(String, int)
instead. sequenceLength is required for the object to be considered valid.htsjdk.tribble.readers.AsciiLineReader(InputStream) 8/8/2017 useAsciiLineReader.from(java.io.InputStream)
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Enum Constants Enum Constant Description htsjdk.samtools.SAMFlag.NOT_PRIMARY_ALIGNMENT useSAMFlag.SECONDARY_ALIGNMENT
instead.