Package htsjdk.samtools.filter


package htsjdk.samtools.filter
  • Class
    Description
    Javascript filter with HEADER type containing TYPE records.
    Aggregates multiple filters and provides a method for applying them all to a given record with one method call.
    Filter to either include or exclude aligned reads $Id$
    Filter out SAMRecords with DuplicateRead flag set $Id$
    Filter for filtering out reads that do not pass the quality filter $Id$
    Deprecated.
    Filtering Iterator which takes a filter and an iterator and iterates through only those records which are not rejected by the filter.
    Filter things that fall outside a specified range of insert sizes.
    Filter SAMRecords so that only those that overlap the given list of intervals.
    Filter out SAMRecords where neither record of a pair overlaps a given set of intervals.
    Wraps an existing filter and inverts it.
    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 )
    Filter things with low mapping quality.
    Deprecated.
    Filters out reads with very few unclipped bases, likely due to the read coming from a foreign organism, e.g.
    Filter by a set of specified readnames
    API for filtering SAMRecords $Id$
    SamRecordFilter that filters out secondary alignments, but not supplemental alignments.
    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 to determine whether a read is "noisy" due to a poly-A run that is a sequencing artifact.
    Filter class for matching tag attributes in SAMRecords $Id$
    Filter SAMRecords so that only those that have at least one un-clipped base are returned.