Class HtsgetBAMDecoderV1_2
java.lang.Object
htsjdk.beta.codecs.reads.htsget.HtsgetBAMDecoder
htsjdk.beta.codecs.reads.htsget.htsgetBAMV1_2.HtsgetBAMDecoderV1_2
- All Implemented Interfaces:
HtsDecoder<SAMFileHeader,
,SAMRecord> HtsQuery<SAMRecord>
,ReadsDecoder
,ReadsQuery<SAMRecord>
,Closeable
,AutoCloseable
,Iterable<SAMRecord>
Version 1.2 of
BundleResourceType.READS_HTSGET_BAM
decoder.-
Constructor Summary
ConstructorDescriptionHtsgetBAMDecoderV1_2
(Bundle inputBundle, ReadsDecoderOptions decoderOptions) -
Method Summary
Modifier and TypeMethodDescriptionvoid
close()
Close any resources associated with this decoder.Get the file header for this decoder.boolean
hasIndex()
Return true if the underlying resource has an index.boolean
Gte true if the underlying resource is queryable.iterator()
Get an iterator of all records in the underlying resource.Get an iterator over all records from the underlying resource that match the query stringquery
(List<HtsInterval> intervals, HtsQueryRule queryRule) Get an iterator over all records from the underlying resource that match the query arguments.Fetch the mate for the given read.queryStart
(String queryName, long start) Get an iterator over all records from the underlying resource that overlap the start positionGet an iterator of unmapped reads.Methods inherited from class htsjdk.beta.codecs.reads.htsget.HtsgetBAMDecoder
getDisplayName, getFileFormat, getInputBundle, getReadsDecoderOptions, getVersion
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface htsjdk.beta.plugin.interval.HtsQuery
query, query, queryContained, queryContained, queryContained, queryOverlapping, queryOverlapping, queryOverlapping
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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HtsgetBAMDecoderV1_2
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Method Details
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getHeader
Description copied from interface:HtsDecoder
Get the file header for this decoder.- Returns:
- the file header for this decoder, of type
H
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close
public void close()Description copied from interface:HtsDecoder
Close any resources associated with this decoder. -
iterator
Description copied from interface:HtsQuery
Get an iterator of all records in the underlying resource.- Returns:
- an iterator of all records in the underlying resource
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isQueryable
public boolean isQueryable()Description copied from interface:HtsQuery
Gte true if the underlying resource is queryable.- Returns:
- true if the underlying resource is queryable. this may be true even if the underlying
resource returns false for
HtsQuery.hasIndex()
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hasIndex
public boolean hasIndex()Description copied from interface:HtsQuery
Return true if the underlying resource has an index.- Returns:
- true if the underlying resource has an index
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query
Description copied from interface:HtsQuery
Get an iterator over all records from the underlying resource that match the query string- Parameters:
queryString
- decoder specific query string- Returns:
- an iterator over all records from the underlying resource that match the query string
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query
Description copied from interface:HtsQuery
Get an iterator over all records from the underlying resource that match the query arguments. Callers much ensure that the intervals are in increasing order and do not overlap or abut.- Parameters:
intervals
- list of intervals to matchqueryRule
- query rule to use, fromHtsQueryRule
- Returns:
- an iterator over all records from the underlying resource that match the query arguments
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queryStart
Description copied from interface:HtsQuery
Get an iterator over all records from the underlying resource that overlap the start position- Parameters:
queryName
- name to matchstart
- start position to overlap- Returns:
- an iterator over all records from the underlying resource that overlap the start position
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queryUnmapped
Description copied from interface:ReadsDecoder
Get an iterator of unmapped reads. Requires an index resource to be included in the inputBundle
. -
queryMate
Description copied from interface:ReadsDecoder
Fetch the mate for the given read. Requires an index resource to be included in the inputBundle
.- Parameters:
rec
- the source record- Returns:
- the source record's mate, or Optional.empty() if the source record has no mate
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