Interface | Description |
---|---|
SamRecordFilter |
API for filtering SAMRecords
$Id$
|
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.
|