# Package htsjdk.samtools.filter

package htsjdk.samtools.filter

Related Packages
Package
Description
htsjdk.samtools
Class
Description
AbstractJavascriptFilter<HEADER,TYPE>
Javascript filter with HEADER type containing TYPE records.
AggregateFilter
Aggregates multiple filters and provides a method for applying them all to a given record with one method call.
AlignedFilter
Filter to either include or exclude aligned reads $Id$
DuplicateReadFilter
Filter out SAMRecords with DuplicateRead flag set $Id$
FailsVendorReadQualityFilter
Filter for filtering out reads that do not pass the quality filter $Id$
FilteringIterator
Deprecated.
use `FilteringSamIterator` instead
FilteringSamIterator
Filtering Iterator which takes a filter and an iterator and iterates through only those records which are not rejected by the filter.
InsertSizeFilter
Filter things that fall outside a specified range of insert sizes.
IntervalFilter
Filter SAMRecords so that only those that overlap the given list of intervals.
IntervalKeepPairFilter
Filter out SAMRecords where neither record of a pair overlaps a given set of intervals.
InvertFilter
Wraps an existing filter and inverts it.
JavascriptSamRecordFilter
JavaScript-based `SamRecordFilter`.
MappingQualityFilter
Filter things with low mapping quality.
NotPrimaryAlignmentFilter
Deprecated.
use `SecondaryAlignmentFilter` instead.
OverclippedReadFilter
Filters out reads with very few unclipped bases, likely due to the read coming from a foreign organism, e.g.
ReadNameFilter
Filter by a set of specified readnames
SamRecordFilter
API for filtering SAMRecords $Id$
SecondaryAlignmentFilter
SamRecordFilter that filters out secondary alignments, but not supplemental alignments.
SecondaryOrSupplementaryFilter
Filter out SAMRecords with Secondary 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 $Id$
SolexaNoiseFilter
Filter to determine whether a read is "noisy" due to a poly-A run that is a sequencing artifact.
TagFilter
Filter class for matching tag attributes in SAMRecords $Id$
WholeReadClippedFilter
Filter SAMRecords so that only those that have at least one un-clipped base are returned.