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Package org.broad.igv.tools

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