Package | Description |
---|---|
htsjdk.samtools.filter | |
htsjdk.samtools.util |
Modifier and Type | Class and Description |
---|---|
class |
AggregateFilter
Aggregates multiple filters and provides a method for applying them all to a given record with
one method call.
|
class |
AlignedFilter
Filter to either include or exclude aligned reads
$Id$
|
class |
DuplicateReadFilter
Filter out SAMRecords with DuplicateRead flag set
$Id$
|
class |
FailsVendorReadQualityFilter
Filter for filtering out reads that do not pass the quality filter
$Id$
|
class |
InsertSizeFilter
Filter things that fall outside a specified range of insert sizes.
|
class |
IntervalFilter
Filter SAMRecords so that only those that overlap the given list of intervals.
|
class |
JavascriptSamRecordFilter
javascript based read filter
The script puts the following variables in the script context:
- 'record' a SamRecord (
https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/samtools/
SAMRecord.java ) - 'header' (
https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/samtools/
SAMFileHeader.java )
|
class |
MappingQualityFilter
Filter things with low mapping quality.
|
class |
NotPrimaryAlignmentFilter
Filter out SAMRecords with NotPrimaryAlignment flag set
$Id$
|
class |
OverclippedReadFilter
Filters out reads with very few unclipped bases, likely due to the read coming
from a foreign organism, e.g.
|
class |
ReadNameFilter
Filter by a set of specified readnames
$Id$
|
class |
SecondaryAlignmentFilter
SamRecordFilter that filters out secondary alignments, but not supplemental alignments.
|
class |
SecondaryOrSupplementaryFilter
Filter out SAMRecords with NotPrimaryAlignment or Supplementary flag set
This class should be viewed as a replacement for NotPrimarySkippingIterator,
in that we did not want to change the functionality of NPSI to no longer match its name
$Id$
|
class |
SolexaNoiseFilter
Filter to determine whether a read is "noisy" due to a poly-A run that is a sequencing artifact.
|
class |
TagFilter
Filter class for matching tag attributes in SAMRecords
$Id$
|
class |
WholeReadClippedFilter
Filter SAMRecords so that only those that have at least one un-clipped base are
returned.
|
Constructor and Description |
---|
FilteringIterator(Iterator<SAMRecord> iterator,
SamRecordFilter filter)
Constructor
|
FilteringIterator(Iterator<SAMRecord> iterator,
SamRecordFilter filter,
boolean filterByPair)
Constructor
|
Constructor and Description |
---|
AggregateFilter(List<SamRecordFilter> filters)
Constructor
|
Modifier and Type | Method and Description |
---|---|
void |
SamLocusIterator.setSamFilters(List<SamRecordFilter> samFilters)
Controls which, if any, SAMRecords are filtered.
|