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

P

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

Peek the sequence name

Peeker - Class in net.sf.snver.pileup.loader

Robust iterator for Bam to integrate with reference and filter

Created by IntelliJ IDEA.

Peeker(FastaReader, Filter, SAMFileReader, Properties, String) - Constructor for class net.sf.snver.pileup.loader.Peeker

Constructor

Peeker(FastaReader, Properties) - Constructor for class net.sf.snver.pileup.loader.Peeker

Constructor

pileup(String[]) - Method in class net.sf.snver.pileup.SNVerIndividual

pileup

pileup(String[]) - Method in class net.sf.snver.pileup.SNVerPool

pileup

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

Pool for pileup process which use the SAMSequenceVo to generate SnverMeta

Created by IntelliJ IDEA.

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

Constructor

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

PoolConfigurationFactory - Class in net.sf.snver.pileup.config

Created by IntelliJ IDEA.

PoolConfigurationFactory() - Constructor for class net.sf.snver.pileup.config.PoolConfigurationFactory

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

Created by IntelliJ IDEA.

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

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

Return a Pair for a single base and score pair

POST_FIX - Static variable in class net.sf.snver.pileup.SNVerIndividual

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

Print meta information into vcf file

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

Print some of information

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

Print count information

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

Print the count file Header for debug

printHeader(PrintWriter, String) - Static method in class net.sf.snver.pileup.core.CoreAnalysis

Print the vcf header

printoutIndividual(String, String, String, double, String, int, int, double, double, int, int, int, int, double, double, double, PrintWriter) - Method in class net.sf.snver.pileup.core.CoreAnalysis

Print for individual vcf file

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

Deprecated.