Package htsjdk.samtools

Class SAMLineParser

  • public class SAMLineParser
extends Object
    This class enables creation of a SAMRecord object from a String in SAM text format. The SAM flag field will be inferred for each record separately, unless the expected format is set using `withSamFlagField`.

    • Constructor Detail

      • SAMLineParser

        public SAMLineParser​(SAMFileHeader samFileHeader)
        Public constructor. Use the default SAMRecordFactory and stringency.
        Parameters:
        samFileHeader - SAM file header

      • SAMLineParser

        public SAMLineParser​(SAMFileHeader samFileHeader,
                     SamReader samFileReader,
                     File samFile)
        Public constructor. Use the default SAMRecordFactory and stringency.
        Parameters:
        samFileHeader - SAM file header
        samFileReader - SAM file reader For passing to SAMRecord.setFileSource, may be null.
        samFile - SAM file being read (for error message only, may be null)

      • SAMLineParser

        public SAMLineParser​(SAMRecordFactory samRecordFactory,
                     ValidationStringency validationStringency,
                     SAMFileHeader samFileHeader,
                     SamReader samFileReader,
                     File samFile)
        Public constructor.
        Parameters:
        samRecordFactory - SamRecord Factory
        validationStringency - validation stringency
        samFileHeader - SAM file header
        samFileReader - SAM file reader For passing to SAMRecord.setFileSource, may be null.
        samFile - SAM file being read (for error message only, may be null)

    • Method Detail

      • getFileHeader

        public SAMFileHeader getFileHeader()
        Get the File header.
        Returns:
        the SAM file header

      • getValidationStringency

        public ValidationStringency getValidationStringency()
        Get validation stringency.
        Returns:
        validation stringency

      • withSamFlagField

        public SAMLineParser withSamFlagField​(SamFlagField samFlagField)
        Sets the expected SAM flag type expected for all records.

      • parseLine

        public SAMRecord parseLine​(String line)
        Parse a SAM line.
        Parameters:
        line - line to parse
        Returns:
        a new SAMRecord object

      • parseLine

        public SAMRecord parseLine​(String line,
                           int lineNumber)
        Parse a SAM line.
        Parameters:
        line - line to parse
        lineNumber - line number in the file. If the line number is not known can be <=0.
        Returns:
        a new SAMRecord object