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.variant.variantcontext.filter.FilteringIterator
since 2/29/16 use
FilteringVariantContextIterator instead |
htsjdk.samtools.filter.FilteringIterator
use
FilteringSamIterator instead |
htsjdk.samtools.filter.NotPrimaryAlignmentFilter
use
SecondaryAlignmentFilter instead. |
htsjdk.samtools.NotPrimarySkippingIterator
use
SecondaryAlignmentSkippingIterator instead. |
htsjdk.samtools.SAMTagUtil
as of 11/2018, the functions in this class have been absorbed by the
SAMTag enum. |
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.SQTagUtil
since 11/2018. SQ is a reserved tag that shouldn't be used and this code untested.
|
htsjdk.samtools.util.StringLineReader |
htsjdk.samtools.apps.TimeChannel
This is deprecated with no replacement. 1/19
|
htsjdk.samtools.apps.TimeRandomAccessFile
This is deprecated with no replacement. 1/19
|
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.MergingSamRecordIterator(SamFileHeaderMerger, boolean) |
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder) |
htsjdk.samtools.SamFileHeaderMerger(Collection<SamReader>, SAMFileHeader.SortOrder, boolean) |
htsjdk.samtools.SAMRecordDuplicateComparator(List<SAMFileHeader>) |
htsjdk.samtools.SAMSequenceRecord(String)
Use
SAMSequenceRecord(String, int) instead.
sequenceLength is required for the object to be considered valid. |
Enum Constant and Description |
---|
htsjdk.samtools.SAMReadGroupRecord.PlatformValue.BGI
Use SAMReadGroupRecord.PlatformValue.DNBSEQ instead.
|
htsjdk.samtools.SAMTag.GC
for backwards compatibility only
|
htsjdk.samtools.SAMTag.GQ
for backwards compatibility only
|
htsjdk.samtools.SAMTag.GS
for backwards compatibility only
|
htsjdk.samtools.SAMTag.MF
for backwards compatibility only
|
htsjdk.samtools.SAMFlag.NOT_PRIMARY_ALIGNMENT
use
SAMFlag.SECONDARY_ALIGNMENT instead. |
htsjdk.samtools.SAMReadGroupRecord.PlatformValue.OTHER
OTHER is not an official value. It is recommended to omit PL if it is not in this list or is unknown.
|
htsjdk.samtools.SAMTag.RT
use BC instead, for backwards compatibilty only
|
htsjdk.samtools.SAMTag.S2
for backwards compatibility only
|
htsjdk.samtools.SAMTag.SQ
for backwards compatibility only
|