Package htsjdk.samtools.filter
package htsjdk.samtools.filter
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ClassDescriptionAbstractJavascriptFilter<HEADER,
TYPE> 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.useSecondaryAlignmentFilter
instead.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 readnamesAPI 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 forNotPrimarySkippingIterator
, 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.
FilteringSamIterator
instead