Package htsjdk.samtools.reference
Class FastaSequenceIndexCreator
- java.lang.Object
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- htsjdk.samtools.reference.FastaSequenceIndexCreator
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public final class FastaSequenceIndexCreator extends Object
Static methods to create anFastaSequenceIndex
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static FastaSequenceIndex
buildFromFasta(Path fastaFile)
Builds a FastaSequenceIndex on the fly from a FASTA file.static void
create(Path fastaFile, boolean overwrite)
Creates a FASTA .fai index for the provided FASTA.
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Method Detail
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create
public static void create(Path fastaFile, boolean overwrite) throws IOException
Creates a FASTA .fai index for the provided FASTA.- Parameters:
fastaFile
- the file to build the index from.overwrite
- if the .fai index already exists override it iftrue
; otherwise, throws aSAMException
.- Throws:
SAMException
- if the fai file already exists or the file is malformed.IOException
- if an IO error occurs.
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buildFromFasta
public static FastaSequenceIndex buildFromFasta(Path fastaFile) throws IOException
Builds a FastaSequenceIndex on the fly from a FASTA file.Note: this also allows to create an index for a compressed file, but does not generate the .gzi index required for use it with samtools. To generate that index, use
GZIIndex.buildIndex(Path)
.- Parameters:
fastaFile
- the FASTA file.- Returns:
- a fai index.
- Throws:
SAMException
- for formatting errors.IOException
- if an IO error occurs.
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