public class VCFUtils extends Object
Constructor and Description |
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VCFUtils() |
Modifier and Type | Method and Description |
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static List<VCFContigHeaderLine> |
makeContigHeaderLines(SAMSequenceDictionary refDict,
File referenceFile)
Create VCFHeaderLines for each refDict entry, and optionally the assembly if referenceFile != null
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static Set<VCFHeaderLine> |
smartMergeHeaders(Collection<VCFHeader> headers,
boolean emitWarnings) |
static VCFHeader |
withUpdatedContigs(VCFHeader oldHeader,
File referenceFile,
SAMSequenceDictionary refDict)
Add / replace the contig header lines in the VCFHeader with the in the reference file and master reference dictionary
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static Set<VCFHeaderLine> |
withUpdatedContigsAsLines(Set<VCFHeaderLine> oldLines,
File referenceFile,
SAMSequenceDictionary refDict) |
static Set<VCFHeaderLine> |
withUpdatedContigsAsLines(Set<VCFHeaderLine> oldLines,
File referenceFile,
SAMSequenceDictionary refDict,
boolean referenceNameOnly) |
public static Set<VCFHeaderLine> smartMergeHeaders(Collection<VCFHeader> headers, boolean emitWarnings) throws IllegalStateException
IllegalStateException
public static VCFHeader withUpdatedContigs(VCFHeader oldHeader, File referenceFile, SAMSequenceDictionary refDict)
oldHeader
- the header to updatereferenceFile
- the file path to the reference sequence used to generate this vcfrefDict
- the SAM formatted reference sequence dictionarypublic static Set<VCFHeaderLine> withUpdatedContigsAsLines(Set<VCFHeaderLine> oldLines, File referenceFile, SAMSequenceDictionary refDict)
public static Set<VCFHeaderLine> withUpdatedContigsAsLines(Set<VCFHeaderLine> oldLines, File referenceFile, SAMSequenceDictionary refDict, boolean referenceNameOnly)
public static List<VCFContigHeaderLine> makeContigHeaderLines(SAMSequenceDictionary refDict, File referenceFile)
refDict
- reference dictionaryreferenceFile
- for assembly name. May be null