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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.apps.TimeChannel This is deprecated with no replacement. 1/19htsjdk.samtools.apps.TimeRandomAccessFile This is deprecated with no replacement. 1/19htsjdk.samtools.filter.FilteringIterator useFilteringSamIterator
insteadhtsjdk.samtools.filter.NotPrimaryAlignmentFilter useSecondaryAlignmentFilter
instead.htsjdk.samtools.NotPrimarySkippingIterator useSecondaryAlignmentSkippingIterator
instead.htsjdk.samtools.SAMTagUtil as of 11/2018, the functions in this class have been absorbed by theSAMTag
enum.htsjdk.samtools.SQTagUtil since 11/2018. SQ is a reserved tag that shouldn't be used and this code untested.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.htsjdk.samtools.SAMTag.GC for backwards compatibility onlyhtsjdk.samtools.SAMTag.GQ for backwards compatibility onlyhtsjdk.samtools.SAMTag.GS for backwards compatibility onlyhtsjdk.samtools.SAMTag.MF for backwards compatibility onlyhtsjdk.samtools.SAMTag.RT use BC instead, for backwards compatibilty onlyhtsjdk.samtools.SAMTag.S2 for backwards compatibility onlyhtsjdk.samtools.SAMTag.SQ for backwards compatibility only