Package htsjdk.samtools.filter

Interface Summary

Interface	Description
SamRecordFilter	API for filtering SAMRecords $Id$

Class Summary

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
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.
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 )
MappingQualityFilter	Filter things with low mapping quality.
NotPrimaryAlignmentFilter	Filter out SAMRecords with NotPrimaryAlignment flag set $Id$
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 $Id$
SecondaryAlignmentFilter	SamRecordFilter that filters out secondary alignments, but not supplemental alignments.
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 $Id$
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.