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GenotypesContext.add(Genotype)
for important information about this functions
constraints and performance costs
indexExtension
to the filepath
, preserving
query string elements if present.
AsciiLineReader.readLine()
functionality around a PositionalBufferedStream
BufferedReader
and its BufferedReader.readLine()
method should be used in preference to this class (when the
LocationAware
functionality is not required) because it offers greater performance.AsciiLineReader
.SAMSequenceDictionary.equals(Object)
-assertion: instead of calling SAMSequenceRecord.equals(Object)
on constituent
SAMSequenceRecord
s in this dictionary against its pair in the target dictionary, in order, call
SAMSequenceRecord.isSameSequence(SAMSequenceRecord)
.
BEDCodec.BEDCodec(StartOffset)
with an argument
of StartOffset.ONE
FeatureCodec
s that read from PositionalBufferedStream
s.VariantContext
by dividing its "AN" by its "AC".
program
in front of the first "head" item in the list of
SAMProgramRecords in header
.
obj
if it implements Closeable
objs
that implement Closeable
SOURCE
.
true
if this HashMap maps one or more keys to this
value.
BAMFileReader
analogue for CRAM files.Feature
from the SOURCE
, reading no further in the underlying source than beyond that feature.
SamReaderFactory.Option
s, then returns itself.
IndexFactory.IndexBalanceApproach
and
the characteristics of the file.Object.toString()
of the provided value if it isn't null; "" otherwise.
SamReaderFactory.Option
s, then returns itself.
Lazy
JexlEngine
instance to avoid class-loading issues.
Interval.compareTo(Interval)
.
outputStreamString
to the process output stream if it is not null, then writes stderr to log.error
and stdout to log.info and blocks until the command is complete.
VariantContextBuilder.filters
LineReaderUtil.fromBufferedStream(java.io.InputStream, LineReaderUtil.LineReaderOption)
, but the synchronicity
option is determined by Defaults
: if asynchronous I/O is enabled, an asynchronous line reader will be
returned.
IntervalList.fromFile(java.io.File)
on the provided files, and returns their IntervalList.union(java.util.Collection)
.
Lazy
, initializing it if necessary.
SeekableStream
which wraps the input stream
using the default buffer size
SeekableStream
which wraps the input stream
FeatureCodec
instance appropriate for the given
featureFile
.
AbstractFeatureReader.getFeatureReader(String, FeatureCodec, boolean)
with requireIndex
= true
AbstractFeatureReader.getFeatureReader(String, String, FeatureCodec, boolean)
with null
for indexResource
AsciiLineReaderIterator.next()
in
the underlying AsciiLineReader
.
filename
Does not actually create an index
file
Does not actually create an index
SamReader.Indexing
facet of this SamReader
.
20
and 0.75
respectively.
0.75
.
SOURCE
has more data.
SeekableStream
s based on URLs/paths.(getNotPrimaryAlignmentFlag() || getSupplementaryAlignmentFlag())
.
GenotypesContext.GenotypesContext(java.util.ArrayList, java.util.Map, java.util.List)
indices
LineReader
s.user [username]
and pass
[password]
.
BufferedReader
with improved performance reading files with long lines.SamReaderFactory.Option
s, ValidationStringency.DEFAULT_STRINGENCY
, and
DefaultSAMRecordFactory
.
SamReaderFactory
.
PositionalBufferedStream
is already LocationAware
.
LocationAware
reader of type SOURCE
.
SOURCE
appropriate for use by this codec from the generic input stream.
Object.toString()
value.
java.util.Objects
for non-JDK7 support.SamInputResource
reading from the provided resource, with no index.
SamInputResource
reading from the provided resource, with no index.
SamInputResource
reading from the provided resource, with no index.
SamInputResource
reading from the provided resource, with no index.
SamInputResource
from a string specifying *either* a url or a file path
SamReaderFactory
InputStream
which performs it's own buffering, and keeps track of the position.key
to the specified value
in this hashtable.
AsciiLineReader.readLine(PositionalBufferedStream)
but uses the stream provided in the constructor
URLHelper
class to be used for URL operations.
Iso8601Date
, but also comes in a "lazy now" flavor.this.remove(Integer)
SAMRecord
s and associated information.SamReader.PrimitiveSamReaderToSamReaderAdapter
.SamReader.PrimitiveSamReader
that expands its functionality into a SamReader
.SamReader
, and offers a
handful of static generators.SamReaderFactory
options.SAMRecordFactory
to the provided one, then returns itself.
InputStream
s encoding SAM dataSeekableStream
s from URL/paths
Applications using this library can set their own factoryIOUtil.slurp(java.io.InputStream, java.nio.charset.Charset)
using the default charset Charset.defaultCharset()
.
IOUtil.slurp(java.io.InputStream, java.nio.charset.Charset)
using the default charset Charset.defaultCharset()
.
Charset
then closes the stream quietly.
clipFrom
, to the SAM record's existing cigar
and, for negative strands, also adjusts the SAM record's start position.
String
representation of this date.
ValidationStringency
to the provided one, then returns itself.
VariantContextWriterBuilder
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