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Package org.broad.igv.tools

Inner Packages
org.broad.igv.tools.converters
org.broad.igv.tools.motiffinder
org.broad.igv.tools.parsers
org.broad.igv.tools.sort
org.broad.igv.tools.ui
org.broad.igv.tools
Abstract
AbstractConsensusCalculator
Calculates the consensus seque nce based on alignments The r ules for defining a conse...
BAMIndexer
CavenerConsensusCalculator
Rules taken from Cavener, Nucl eic Acids Res. 15, 1353-1361, 1987. Also used by CisRE...
CommandLineStatusMonitor
Interface
StatusMonitor
CoverageCounter
Class to compute coverage on a n alignment or feature file. This class is designed to...
FeatureSearcher
Used for searching for the nex t feature, given a source. We simply call getFeature o...
Interface
Runnable
GenomeDesc
IgvTools
Command accessories for IGV.
UI
IgvToolsGui
UI
JDialog
IgvToolsGui$Tool
ListAccumulator
Estimating percentiles -- weig hted average of multiple esti mates
PFMExporter
Export the consensus of alignm ent counts. Format is similar to http://lgsun.grc.nia....
PairedEndStats
PairedUtils
Created by jrobinso on 10/6/15 .
PreprocessingException
RuntimeException
Preprocessor
Interface
DataConsumer
RepeatMaskSplitter
Splits a repeat mask file down loaded from UCSC into multipl e files, one per repeat c...
SAMRecordIterator
SwingWorker
TestFileGenerator
UCSCUtils
WigSummer
Sum the values from a list of wig files and output a new wi g file with the totals. T...