Call R from Java.
Java database connector.
A jar package to calculate p-value.
DatabaseManager is a class to manage database. We make it as a static private class so everyone can only use it in a single thread, which will influence the efficiency, but in order to synchronize, we would like to make it.
TableCreator provides a variety of static methods to create different kinds of tables.
The Class DNAVCFParser can parser DNA VCF file with single or multiple samples in a file, then insert all data into database. Pay attention that the class will delete old sample tables and create new ones for all samples in this DNA VCF file.
The Class RNAVCFParser can parser RNA VCF file with single or multiple samples in a file, then insert all data into database. Pay attention that the class will delete old sample tables and create new ones for all samples in this RNA VCF file..
The Class RNAVCFParser can parser RNA VCF file with single or multiple samples in a file, then insert all data into database. Pay attention that the class will delete old sample tables and create new ones for all samples in this RNA VCF file..
The Class DNAVCFParser can parser DNA VCF file with single or multiple samples in a file, then insert all data into database. Pay attention that the class will delete old sample tables and create new ones for all samples in this DNA VCF file.
The Class EditingTypeFilter is a rule-based filter that user enables to select the type of RNA editing as his preference.
The Class FisherExactTestFilter is a statistical filter to reduce the errors in detecting RNA editing sites caused by technical artifacts (e.g., sequencing errors).
The Class KnownSNPFilter is a rule-based filter that will filter out the site which was known SNP in DNA level for eliminating germline variants.
The Class QualityControlFilter is a rule-based filter to filter RNA editing sites by their quality and coverage of depth.
The Class RepeatRegionsFilter is a rule-based filter. Variants that were within repeat regions were excluded. However, sites in SINE/Alu regions were remained since A-I RNA editing is pervasive in Alu repeats and it has been implicated in human diseases such as breast cancer and Ewing's sarcoma.
 The Class SpliceJunctionFilter is a rule-based filter. Variants that were within+/-k bp (e.g., k = 2) of the splice junction, which were supposed to be unreliable, were excluded based on the gene annotation file.
The Class DNARNAFilter is a rule-based filter. RNA-seq variants where its counterparts in genomic DNA is not reference homozygote (e.g., AA) would be excluded if DNA sequencing data is available.
The Class LikelihoodRatioFilter is a statistical filter to reduce the errors in detecting RNA editing sites caused by technical artifacts (e.g., sequencing errors).
The database preferences stores information relative to database.
SiteBean is a class to parse a strip of all information from a VCF file. It also uses in querying data from database.
This class intends to collect all indexes used in creating table for database.