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SmartFileReader - Class in net.sf.varscan

A class for bug-free file reading with the Java API contributed by Bina Technologies

SmartFileReader(File) - Constructor for class net.sf.varscan.SmartFileReader

SmartFileReader(FileDescriptor) - Constructor for class net.sf.varscan.SmartFileReader

SmartFileReader(String) - Constructor for class net.sf.varscan.SmartFileReader

Somatic - Class in net.sf.varscan

A class for determining somatic status of variants from Normal/Tumor pileup files

Somatic(String[], boolean) - Constructor for class net.sf.varscan.Somatic

Somatic(String[]) - Constructor for class net.sf.varscan.Somatic

somatic(String[], HashMap<String, String>) - Static method in class net.sf.varscan.VarScan

Calls somatic/germline/LOH variants from normal and tumor pileup files

somaticFilter(String[], HashMap<String, String>) - Static method in class net.sf.varscan.VarScan

Filters variants by coverage, significance, frequency, etc.