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#Htsjdk.samtools.filter Classes and Interfaces - 19 results found.
NameDescriptionTypePackageFramework
AbstractJavascriptFilterJavascript filter with HEADER type containing TYPE records.Classhtsjdk.samtools.filterHtsJDK
AggregateFilterClasshtsjdk.samtools.filterHtsJDK
AlignedFilterClasshtsjdk.samtools.filterHtsJDK
DuplicateReadFilterClasshtsjdk.samtools.filterHtsJDK
FailsVendorReadQualityFilterClasshtsjdk.samtools.filterHtsJDK
FilteringIteratorFiltering Iterator which takes a filter and an iterator and iterates through only those records which are not rejected by the filter.Classhtsjdk.samtools.filterHtsJDK
InsertSizeFilterFilter things that fall outside a specified range of insert sizes.Classhtsjdk.samtools.filterHtsJDK
IntervalFilterFilter SAMRecords so that only those that overlap the given list of intervals.Classhtsjdk.samtools.filterHtsJDK
JavascriptSamRecordFilterjavascript based read filter The script puts the following variables in the script context:Classhtsjdk.samtools.filterHtsJDK
MappingQualityFilterFilter things with low mapping quality.Classhtsjdk.samtools.filterHtsJDK
NotPrimaryAlignmentFilterClasshtsjdk.samtools.filterHtsJDK
OverclippedReadFilterFilters out reads with very few unclipped bases, likely due to the read coming from a foreign organism, e.Classhtsjdk.samtools.filterHtsJDK
ReadNameFilterClasshtsjdk.samtools.filterHtsJDK
SamRecordFilterAPI for filtering SAMRecordsDetermines whether a SAMRecord matches this filterInterfacehtsjdk.samtools.filterHtsJDK
SecondaryAlignmentFilterSamRecordFilter that filters out secondary alignments, but not supplemental alignments.Classhtsjdk.samtools.filterHtsJDK
SecondaryOrSupplementaryFilterFilter out SAMRecords with NotPrimaryAlignment or Supplementary flag set This class should be viewed as a replacement for NotPrimarySkippingIterator,Classhtsjdk.samtools.filterHtsJDK
SolexaNoiseFilterFilter to determine whether a read is "noisy" due to a poly-A run that is a sequencing artifact.Classhtsjdk.samtools.filterHtsJDK
TagFilterClasshtsjdk.samtools.filterHtsJDK
WholeReadClippedFilterFilter SAMRecords so that only those that have at least one un-clipped base areAuthor:ktibbett@broadinstitute.Classhtsjdk.samtools.filterHtsJDK