Allows storage and fast random access to read depths in VCF files derived from bacterial reference mapping.
BugMix includes four main classes:
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vcfStore- parses VCF files, computing minor allele frequencies and storing them in on-disc in indexed sqlite databases, one per vcf file.
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mixtureReader - extracts information from one vcfStore'd item. Various methods are available extracting per-base, per-gene, or per arbitrary position set etc.
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multiMixtureReader - extracts information from multiple vcfStore'd items.
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summaryStore - a helper class used by the mixtureReader and multiMixtureReader classes to persist summary information generated in an RDBMS. - this ensures that computations, which may be expensive, only occur once. - the data is accessible from the RDBMS level but the persistence is transparent if using the mixture & multiMixtureReader classes.
Use cases addressed with this component concern
- the identification of mixed samples of TB.
- identification of regions where mis-mapping may have occurred