HtsQuery (htsjdk 3.0.5 API)

Type Parameters:

RECORD - the type of records/iterators returned by queries

All Superinterfaces:

java.lang.Iterable<RECORD>

All Known Subinterfaces:

HaploidReferenceDecoder, HtsDecoder<H,R>, ReadsDecoder, VariantsDecoder

All Known Implementing Classes:

BAMDecoder, BAMDecoderV1_0, CRAMDecoder, CRAMDecoderV2_1, CRAMDecoderV3_0, FASTADecoderV1_0, HtsgetBAMDecoder, HtsgetBAMDecoderV1_2, SAMDecoder, SAMDecoderV1_0, VCFDecoder, VCFDecoderV3_2, VCFDecoderV3_3, VCFDecoderV4_0, VCFDecoderV4_1, VCFDecoderV4_2, VCFDecoderV4_3
```
public interface HtsQuery<RECORD>
extends java.lang.Iterable<RECORD>
```
Common query interface for HtsDecoders

Method Summary

All Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method and Description
`boolean`	`hasIndex()` Return true if the underlying resource has an index.
`boolean`	`isQueryable()` Gte true if the underlying resource is queryable.
`CloseableIterator<RECORD>`	`iterator()` Get an iterator of all records in the underlying resource.
`default CloseableIterator<RECORD>`	`query(HtsInterval interval, HtsQueryRule queryRule)` Get an iterator over all records from the underlying resource that match the query arguments
`default CloseableIterator<RECORD>`	`query(java.util.List<HtsInterval> intervals, HtsQueryRule queryRule)` Get an iterator over all records from the underlying resource that match the query arguments.
`default CloseableIterator<RECORD>`	`query(java.lang.String queryString)` Get an iterator over all records from the underlying resource that match the query string
`default CloseableIterator<RECORD>`	`query(java.lang.String queryName, long start, long end, HtsQueryRule queryRule)` Get an iterator over all records from the underlying resource that match the query arguments
`default CloseableIterator<RECORD>`	`queryContained(HtsInterval interval)` Get an iterator over all records from the underlying resource that are contained within the query interval
`default CloseableIterator<RECORD>`	`queryContained(java.util.List<HtsInterval> intervals)` Get an iterator over all records from the underlying resource that are contained within the query intervals
`default CloseableIterator<RECORD>`	`queryContained(java.lang.String queryName, long start, long end)` Gte an iterator over all records from the underlying resource that match the query arguments
`default CloseableIterator<RECORD>`	`queryOverlapping(HtsInterval interval)` Get an iterator over all records from the underlying resource that overlap the query interval
`default CloseableIterator<RECORD>`	`queryOverlapping(java.util.List<HtsInterval> intervals)` Get an iterator over all records from the underlying resource that overlap the query intervals
`default CloseableIterator<RECORD>`	`queryOverlapping(java.lang.String queryName, long start, long end)` Get an iterator over all records from the underlying resource that match the query arguments
`default CloseableIterator<RECORD>`	`queryStart(java.lang.String queryName, long start)` Get an iterator over all records from the underlying resource that overlap the start position

Methods inherited from interface java.lang.Iterable
forEach, spliterator

- Method Detail
  - iterator
```
CloseableIterator<RECORD> iterator()
```
    Get an iterator of all records in the underlying resource.
    
    Specified by:
    
    iterator in interface java.lang.Iterable<RECORD>
    
    Returns:
    
    an iterator of all records in the underlying resource
  - isQueryable
```
boolean isQueryable()
```
    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 hasIndex()
  - hasIndex
```
boolean hasIndex()
```
    Return true if the underlying resource has an index.
    
    Returns:
    
    true if the underlying resource has an index
  - query
```
default CloseableIterator<RECORD> query(java.lang.String queryString)
```
    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
  - query
```
default CloseableIterator<RECORD> query(java.lang.String queryName,
                                        long start,
                                        long end,
                                        HtsQueryRule queryRule)
```
    Get an iterator over all records from the underlying resource that match the query arguments
    
    Parameters:
    
    queryName - name to match
    
    start - start of query interval
    
    end - end of query interval
    
    queryRule - query rule value to use (from HtsQueryRule
    
    Returns:
    
    an iterator over all records from the underlying resource that match the query arguments
  - queryOverlapping
```
default CloseableIterator<RECORD> queryOverlapping(java.lang.String queryName,
                                                   long start,
                                                   long end)
```
    Get an iterator over all records from the underlying resource that match the query arguments
    
    Parameters:
    
    queryName - name to match
    
    start - start of query interval
    
    end - end of query interval
    
    Returns:
    
    an iterator over all records from the underlying resource that match the query arguments
  - queryContained
```
default CloseableIterator<RECORD> queryContained(java.lang.String queryName,
                                                 long start,
                                                 long end)
```
    Gte an iterator over all records from the underlying resource that match the query arguments
    
    Parameters:
    
    queryName - name to match
    
    start - start of query interval
    
    end - end of query interval
    
    Returns:
    
    an iterator over all records from the underlying resource that match the query arguments
  - query
```
default CloseableIterator<RECORD> query(HtsInterval interval,
                                        HtsQueryRule queryRule)
```
    Get an iterator over all records from the underlying resource that match the query arguments
    
    Parameters:
    
    interval - interval to match
    
    queryRule - query rule to use, from HtsQueryRule
    
    Returns:
    
    an iterator over all records from the underlying resource that match the query arguments
  - queryOverlapping
```
default CloseableIterator<RECORD> queryOverlapping(HtsInterval interval)
```
    Get an iterator over all records from the underlying resource that overlap the query interval
    
    Parameters:
    
    interval - interval to match
    
    Returns:
    
    an iterator over all records from the underlying resource that overlap the query interval
  - queryContained
```
default CloseableIterator<RECORD> queryContained(HtsInterval interval)
```
    Get an iterator over all records from the underlying resource that are contained within the query interval
    
    Parameters:
    
    interval - interval to match
    
    Returns:
    
    an iterator over all records from the underlying resource that are contained within the query interval
  - query
```
default CloseableIterator<RECORD> query(java.util.List<HtsInterval> intervals,
                                        HtsQueryRule queryRule)
```
    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 match
    
    queryRule - query rule to use, from HtsQueryRule
    
    Returns:
    
    an iterator over all records from the underlying resource that match the query arguments
  - queryOverlapping
```
default CloseableIterator<RECORD> queryOverlapping(java.util.List<HtsInterval> intervals)
```
    Get an iterator over all records from the underlying resource that overlap the query intervals
    
    Parameters:
    
    intervals - list of intervals to use
    
    Returns:
    
    an iterator over all records from the underlying resource that overlap the query intervals
  - queryContained
```
default CloseableIterator<RECORD> queryContained(java.util.List<HtsInterval> intervals)
```
    Get an iterator over all records from the underlying resource that are contained within the query intervals
    
    Parameters:
    
    intervals - list of intervals to use
    
    Returns:
    
    an iterator over all records from the underlying resource that are contained within the query intervals
  - queryStart
```
default CloseableIterator<RECORD> queryStart(java.lang.String queryName,
                                             long start)
```
    Get an iterator over all records from the underlying resource that overlap the start position
    
    Parameters:
    
    queryName - name to match
    
    start - start position to overlap
    
    Returns:
    
    an iterator over all records from the underlying resource that overlap the start position

Interface HtsQuery<RECORD>

Method Summary

Methods inherited from interface java.lang.Iterable

Method Detail

iterator

isQueryable

hasIndex

query

query

queryOverlapping

queryContained

query

queryOverlapping

queryContained

query

queryOverlapping

queryContained

queryStart