Package htsjdk.samtools.filter

Javascript filter with HEADER type containing TYPE records.

Filter to either include or exclude aligned reads $Id$

Filter for filtering out reads that do not pass the quality filter $Id$

Filtering Iterator which takes a filter and an iterator and iterates through only those records which are not rejected by the filter.

Filter SAMRecords so that only those that overlap the given list of intervals.

Wraps an existing filter and inverts it.

Filter things with low mapping quality.

Filters out reads with very few unclipped bases, likely due to the read coming from a foreign organism, e.g.

API for filtering SAMRecords $Id$

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 $Id$

Filter class for matching tag attributes in SAMRecords $Id$