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

C

checkRecord(SAMRecord) - Method in class net.sf.snver.pileup.meta.SAMSequenceVoFactory

close() - Method in class net.sf.snver.pileup.core.CoreAnalysis

Close the file handler

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

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

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

compute(String, char, int) - Method in class net.sf.snver.pileup.meta.PileupPool

Generate SnverMeta Object from pool

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

Ini file loader

Created by IntelliJ IDEA.

ConfigureReader(String, String) - Constructor for class net.sf.snver.pileup.loader.ConfigureReader

Deprecated.

ConfigureReader(int, String) - Constructor for class net.sf.snver.pileup.loader.ConfigureReader

Deprecated.

ConfigureReader(Properties) - Constructor for class net.sf.snver.pileup.loader.ConfigureReader

CoreAnalysis - Class in net.sf.snver.pileup.core

Core analysis algorithm

Created by IntelliJ IDEA.

CoreAnalysis() - Constructor for class net.sf.snver.pileup.core.CoreAnalysis

createProperties(String[]) - Method in class net.sf.snver.pileup.config.AbstractConfigurationFactory

Update the user input properties onto the default properties object

createSequenceByCigar(SAMRecord) - Method in class net.sf.snver.pileup.meta.SAMSequenceVoFactory

CUT_OFF - Static variable in class net.sf.snver.pileup.config.Dictionary