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

S

SAMSequenceVo - Class in net.sf.snver.pileup.meta

Facade Object to present the SAM Record

Created by IntelliJ IDEA.

SAMSequenceVo(SAMRecord) - Constructor for class net.sf.snver.pileup.meta.SAMSequenceVo

Constructor

SAMSequenceVoFactory - Class in net.sf.snver.pileup.meta

Created by IntelliJ IDEA.

setMappingQualityThreshold(int) - Method in class net.sf.snver.pileup.meta.SAMSequenceVoFactory

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

setMore(Properties) - Method in class net.sf.snver.pileup.config.IndividualConfigurationFactory

setMore(Properties) - Method in class net.sf.snver.pileup.config.PoolConfigurationFactory

Simen - Class in net.sf.snver.pileup.util.math

Simen() - Constructor for class net.sf.snver.pileup.util.math.Simen

simes(ArrayList) - Static method in class net.sf.snver.pileup.util.math.Simen

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

Return the pool size

size() - Method in class net.sf.snver.pileup.util.Filter

Return filter pool size

skip() - Method in class net.sf.snver.pileup.meta.PileupPool

Skip the useless position

SNVerIndividual - Class in net.sf.snver.pileup

Created by IntelliJ IDEA.

SNVerIndividual() - Constructor for class net.sf.snver.pileup.SNVerIndividual

SnverMeta - Class in net.sf.snver.pileup.meta

Position based countable object for result Created by IntelliJ IDEA.

SnverMeta(String, int, char, int, String, String) - Constructor for class net.sf.snver.pileup.meta.SnverMeta

Constructor

SnverMeta() - Constructor for class net.sf.snver.pileup.meta.SnverMeta

Null parameter constructor

SnverPileupReaderTest - Class in net.sf.snver.pileup.test

Created by IntelliJ IDEA.

SnverPileupReaderTest() - Constructor for class net.sf.snver.pileup.test.SnverPileupReaderTest

SNVerPool - Class in net.sf.snver.pileup

Created by IntelliJ IDEA.

SNVerPool() - Constructor for class net.sf.snver.pileup.SNVerPool

StrandBias - Class in net.sf.snver.pileup.util.math

StrandBias() - Constructor for class net.sf.snver.pileup.util.math.StrandBias

StrandBias(int, int) - Static method in class net.sf.snver.pileup.util.math.StrandBias

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

Get the set of property names