Class SAMHeaderHadoopUtils


  • public class SAMHeaderHadoopUtils
    extends Object
    This class contains methods and classes related to save and load SAM file header in Hadoop mappers and reducers.
    Since:
    2.0
    Author:
    Laurent Jourdren
    • Constructor Detail

      • SAMHeaderHadoopUtils

        public SAMHeaderHadoopUtils()
    • Method Detail

      • loadSAMHeaders

        public static List<String> loadSAMHeaders​(org.apache.hadoop.mapreduce.JobContext context)
                                           throws IOException
        Load SAM headers.
        Parameters:
        context - the Hadoop context
        Returns:
        a list of String with the SAM headers
        Throws:
        IOException - if an error occurs while loading the headers
      • createSAMSequenceDictionaryFromSAMHeader

        public static htsjdk.samtools.SAMSequenceDictionary createSAMSequenceDictionaryFromSAMHeader​(List<String> headers)
        Create a SAMSequenceDictionary from the SAM header in a list of String.
        Parameters:
        headers - the list of String
        Returns:
        a new SAMSequenceDictionary object with the SAM headers