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class FAIUtils extends AnyRef

Routines for reading a FASTA index (.fai) file efficiently. They can be generated by e.g. 'seqkit faidx'

This algorithm tries to seek to the best position in the FAI file based on the current offset in the fasta file, assuming the records are on average evenly spread out. This is to help performance in the case where FAI files are huge, and we would otherwise need to parse the whole thing for each split. Additional records may be included before or after, so the start position of each record should still be checked.

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  1. new FAIUtils(path: Path, job: Configuration, startByte: Long, fullSize: Long)

    path

    Path to the fai file

    job

    The Hadoop configuration

    startByte

    start byte in the fasta file

    fullSize

    total size of the fasta file

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  9. def fileSize: Long
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  16. def recordsAtOffset: BufferedIterator[FAIRecord]

    Stream FAI records from the current offset in the fai file.

    Stream FAI records from the current offset in the fai file. After use, the close() method must be called to close the underlying source.

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