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