A B C D E F G H I M N O P S T U V

G

getChromosome() - Method in class net.sf.snver.pileup.meta.SnverMeta

Get chromosome name

getCorrectedWeitghtedErrorEstimate(int) - Method in class net.sf.snver.pileup.meta.SnverMeta

getCount(char) - Method in class net.sf.snver.pileup.meta.SnverMeta

Return the count number of base from both sequence

getCumlativeP(int, int, int, int) - Method in class net.sf.snver.pileup.util.math.FisherExact

Calculates the one-tail P-value for the Fisher Exact test.

getDefaultProperties() - Method in class net.sf.snver.pileup.config.AbstractConfigurationFactory

Build default properties object from a template

getErrorEstimate() - Method in class net.sf.snver.pileup.meta.SnverMeta

Return estimated error

getFile(int) - Method in class net.sf.snver.pileup.loader.ConfigureReader

Return file handler by given index

getFileIndex() - Method in class net.sf.snver.pileup.loader.Peeker

Get file index

getFilePath(int) - Method in class net.sf.snver.pileup.loader.ConfigureReader

Return file path by given index

getFilter() - Method in class net.sf.snver.pileup.loader.FilterReader

Return filter handler

getFilter() - Method in class net.sf.snver.pileup.loader.Peeker

Filter Getter

getForwardBaseNum(char) - Method in class net.sf.snver.pileup.meta.SnverMeta

Get the base count from forward sequence

getGnomeChar(int) - Method in class net.sf.snver.pileup.meta.SnverMeta

Return the base character

getIndel() - Method in class net.sf.snver.pileup.meta.SnverMeta

Retunr the indel number

getIndex() - Method in class net.sf.snver.pileup.meta.SnverMeta

Get the index of chromosome

getIndividualUsage() - Static method in class net.sf.snver.pileup.util.Usage

getInstance() - Static method in class net.sf.snver.pileup.core.CoreAnalysis

Get singleton instance

getInstance() - Static method in class net.sf.snver.pileup.meta.SAMSequenceVoFactory

getLeftTailedP(int, int, int, int) - Method in class net.sf.snver.pileup.util.math.FisherExact

Calculates the left-tail P-value for the Fisher Exact test.

getMostAltBase() - Method in class net.sf.snver.pileup.meta.SnverMeta

Get the mose alt base

getMostBase() - Method in class net.sf.snver.pileup.meta.SnverMeta

Get the mose base including ref, if indel is most, return 0

getP(int, int, int, int) - Method in class net.sf.snver.pileup.util.math.FisherExact

calculates the P-value for this specific state

getPoolPvalue(String) - Static method in class net.sf.snver.pileup.util.NumFormat

getPoolUsage() - Static method in class net.sf.snver.pileup.util.Usage

getPosition() - Method in class net.sf.snver.pileup.loader.Peeker

Get current position

getProperties(int) - Method in class net.sf.snver.pileup.loader.ConfigureReader

Return n by given index

getProperties() - Method in class net.sf.snver.pileup.loader.Peeker

Properties Getter

getPropertyType(String) - Static method in class net.sf.snver.pileup.config.Dictionary

Get the property type

getpValue(SnverMeta, Properties) - Method in class net.sf.snver.pileup.core.CoreAnalysis

Calculate P value

getpValue(SnverMeta, int) - Method in class net.sf.snver.pileup.core.CoreAnalysis

Deprecated.

getRatio() - Method in class net.sf.snver.pileup.meta.SnverMeta

Return the alt/ref ratio

getRatioString() - Method in class net.sf.snver.pileup.meta.SnverMeta

Return the alt/ref type

getRef() - Method in class net.sf.snver.pileup.loader.Peeker

Return the current reference base pair

getRef() - Method in class net.sf.snver.pileup.meta.SnverMeta

Get reference

getReferenceSeq(int, String) - Method in class net.sf.snver.pileup.loader.FastaReader

Return the whole genome reference with validation by genome index and name

getReverseBaseNum(char) - Method in class net.sf.snver.pileup.meta.SnverMeta

Get the base count from reverse sequence

getRightTailedP(int, int, int, int) - Method in class net.sf.snver.pileup.util.math.FisherExact

Calculates the right-tail P-value for the Fisher Exact test.

getRightTailedPQuick(int, int, int, int, double) - Method in class net.sf.snver.pileup.util.math.FisherExact

Calculates the right-tail P-value for the Fisher Exact test.

getSequenceName() - Method in class net.sf.snver.pileup.meta.SAMSequenceVo

Get sequence name

getShortName(int) - Method in class net.sf.snver.pileup.loader.ConfigureReader

Return short name of file by given index

getTotal() - Method in class net.sf.snver.pileup.meta.SnverMeta

Return the total number of base, not including indel

getTwoTailedP(int, int, int, int) - Method in class net.sf.snver.pileup.util.math.FisherExact

Calculates the two-tailed P-value for the Fisher Exact test.