Enum SAMValidationError.Type

    • Enum Constant Detail

      • INVALID_QUALITY_FORMAT

        public static final SAMValidationError.Type INVALID_QUALITY_FORMAT
        quality encodings out of range; appear to be Solexa or Illumina when Phread expected
      • INVALID_FLAG_PROPER_PAIR

        public static final SAMValidationError.Type INVALID_FLAG_PROPER_PAIR
        proper pair flag set for unpaired read
      • INVALID_FLAG_MATE_UNMAPPED

        public static final SAMValidationError.Type INVALID_FLAG_MATE_UNMAPPED
        mate unmapped flag set when mate is mapped or not set when mate is not mapped
      • MISMATCH_FLAG_MATE_UNMAPPED

        public static final SAMValidationError.Type MISMATCH_FLAG_MATE_UNMAPPED
        mate unmapped flag does not match read unmapped flag of mate
      • INVALID_FLAG_MATE_NEG_STRAND

        public static final SAMValidationError.Type INVALID_FLAG_MATE_NEG_STRAND
        mate negative strand flag set for unpaired read
      • MISMATCH_FLAG_MATE_NEG_STRAND

        public static final SAMValidationError.Type MISMATCH_FLAG_MATE_NEG_STRAND
        mate negative strand flag does not match read negative strand flag of mate
      • INVALID_FLAG_FIRST_OF_PAIR

        public static final SAMValidationError.Type INVALID_FLAG_FIRST_OF_PAIR
        first of pair flag set for unpaired read
      • INVALID_FLAG_SECOND_OF_PAIR

        public static final SAMValidationError.Type INVALID_FLAG_SECOND_OF_PAIR
        second of pair flag set for unpaired read
      • PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND

        public static final SAMValidationError.Type PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND
        pair flag set but not marked as first or second of pair
      • INVALID_FLAG_NOT_PRIM_ALIGNMENT

        public static final SAMValidationError.Type INVALID_FLAG_NOT_PRIM_ALIGNMENT
        not primary alignment flag set for unmapped read
      • INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT

        public static final SAMValidationError.Type INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT
        supplementary alignment flag set for unmapped read
      • INVALID_FLAG_READ_UNMAPPED

        public static final SAMValidationError.Type INVALID_FLAG_READ_UNMAPPED
        mapped read flat not set for mapped read
      • INVALID_MAPPING_QUALITY

        public static final SAMValidationError.Type INVALID_MAPPING_QUALITY
        mapping quality set for unmapped read or is >= 256
      • INVALID_CIGAR

        public static final SAMValidationError.Type INVALID_CIGAR
        CIGAR string is empty for mapped read or not empty of unmapped read, or other CIGAR badness.
      • ADJACENT_INDEL_IN_CIGAR

        public static final SAMValidationError.Type ADJACENT_INDEL_IN_CIGAR
        CIGAR string contains I followed by D, or vice versa
      • INVALID_MATE_REF_INDEX

        public static final SAMValidationError.Type INVALID_MATE_REF_INDEX
        mate reference index (MRNM) set for unpaired read
      • MISMATCH_MATE_REF_INDEX

        public static final SAMValidationError.Type MISMATCH_MATE_REF_INDEX
        mate reference index (MRNM) does not match reference index of mate
      • INVALID_REFERENCE_INDEX

        public static final SAMValidationError.Type INVALID_REFERENCE_INDEX
        reference index not found in sequence dictionary
      • INVALID_ALIGNMENT_START

        public static final SAMValidationError.Type INVALID_ALIGNMENT_START
        alignment start is can not be correct
      • MISMATCH_MATE_ALIGNMENT_START

        public static final SAMValidationError.Type MISMATCH_MATE_ALIGNMENT_START
        mate alignment does not match alignment start of mate
      • MATE_FIELD_MISMATCH

        public static final SAMValidationError.Type MATE_FIELD_MISMATCH
        the record's mate fields do not match the corresponding fields of the mate
      • INVALID_TAG_NM

        public static final SAMValidationError.Type INVALID_TAG_NM
        the NM tag (nucleotide differences) is incorrect
      • MISSING_TAG_NM

        public static final SAMValidationError.Type MISSING_TAG_NM
        the NM tag (nucleotide differences) is missing
      • MISSING_HEADER

        public static final SAMValidationError.Type MISSING_HEADER
        the sam/bam file is missing the header
      • MISSING_SEQUENCE_DICTIONARY

        public static final SAMValidationError.Type MISSING_SEQUENCE_DICTIONARY
        there is no sequence dictionary in the header
      • MISSING_READ_GROUP

        public static final SAMValidationError.Type MISSING_READ_GROUP
        the header is missing read group information
      • READ_GROUP_NOT_FOUND

        public static final SAMValidationError.Type READ_GROUP_NOT_FOUND
        A read group ID on a SAMRecord is not found in the header
      • RECORD_MISSING_READ_GROUP

        public static final SAMValidationError.Type RECORD_MISSING_READ_GROUP
        A SAMRecord is found with no read group id
      • INVALID_INDEXING_BIN

        public static final SAMValidationError.Type INVALID_INDEXING_BIN
        Indexing bin set on SAMRecord does not agree with computed value.
      • MISMATCH_READ_LENGTH_AND_QUALS_LENGTH

        public static final SAMValidationError.Type MISMATCH_READ_LENGTH_AND_QUALS_LENGTH
      • CIGAR_MAPS_OFF_REFERENCE

        public static final SAMValidationError.Type CIGAR_MAPS_OFF_REFERENCE
        Bases corresponding to M operator in CIGAR are beyond the end of the reference.
      • MISMATCH_READ_LENGTH_AND_E2_LENGTH

        public static final SAMValidationError.Type MISMATCH_READ_LENGTH_AND_E2_LENGTH
        Length of E2 (secondary base calls) and U2 (secondary base quals) tag values should match read length
      • MISMATCH_READ_LENGTH_AND_U2_LENGTH

        public static final SAMValidationError.Type MISMATCH_READ_LENGTH_AND_U2_LENGTH
      • E2_BASE_EQUALS_PRIMARY_BASE

        public static final SAMValidationError.Type E2_BASE_EQUALS_PRIMARY_BASE
        Secondary base calls should not be the same as primary, unless one or the other is N
      • BAM_FILE_MISSING_TERMINATOR_BLOCK

        public static final SAMValidationError.Type BAM_FILE_MISSING_TERMINATOR_BLOCK
        BAM appears to be healthy, but is an older file so doesn't have terminator block.
      • UNRECOGNIZED_HEADER_TYPE

        public static final SAMValidationError.Type UNRECOGNIZED_HEADER_TYPE
        Header record is not one of the standard types
      • POORLY_FORMATTED_HEADER_TAG

        public static final SAMValidationError.Type POORLY_FORMATTED_HEADER_TAG
        Header tag does not have colon
      • HEADER_TAG_MULTIPLY_DEFINED

        public static final SAMValidationError.Type HEADER_TAG_MULTIPLY_DEFINED
        Header tag appears more than once in header line with different value
      • HEADER_RECORD_MISSING_REQUIRED_TAG

        public static final SAMValidationError.Type HEADER_RECORD_MISSING_REQUIRED_TAG
      • HEADER_TAG_NON_CONFORMING_VALUE

        public static final SAMValidationError.Type HEADER_TAG_NON_CONFORMING_VALUE
        Header tag contains illegal value
      • TAG_VALUE_TOO_LARGE

        public static final SAMValidationError.Type TAG_VALUE_TOO_LARGE
        Unsigned integer tag value is deprecated in BAM.
      • INVALID_INDEX_FILE_POINTER

        public static final SAMValidationError.Type INVALID_INDEX_FILE_POINTER
        Invalid virtualFilePointer in index
      • INVALID_PREDICTED_MEDIAN_INSERT_SIZE

        public static final SAMValidationError.Type INVALID_PREDICTED_MEDIAN_INSERT_SIZE
        PI tag value is not numeric.
      • DUPLICATE_READ_GROUP_ID

        public static final SAMValidationError.Type DUPLICATE_READ_GROUP_ID
        Same read group id appears more than once
      • MISSING_PLATFORM_VALUE

        public static final SAMValidationError.Type MISSING_PLATFORM_VALUE
        The read group is missing its PL (platform unit) field
      • INVALID_PLATFORM_VALUE

        public static final SAMValidationError.Type INVALID_PLATFORM_VALUE
        The read group has an invalid value set for its PL field
      • DUPLICATE_PROGRAM_GROUP_ID

        public static final SAMValidationError.Type DUPLICATE_PROGRAM_GROUP_ID
        Same program group id appears more than once
      • MATE_NOT_FOUND

        public static final SAMValidationError.Type MATE_NOT_FOUND
        Read is marked as paired, but its pair was not found.
      • MATES_ARE_SAME_END

        public static final SAMValidationError.Type MATES_ARE_SAME_END
        Both mates are marked as first of pair, or both mates are marked as second of pair.
      • MISMATCH_MATE_CIGAR_STRING

        public static final SAMValidationError.Type MISMATCH_MATE_CIGAR_STRING
        The Cigar String in the MC Tag does not match the Cigar String for the mate of this read.
      • MATE_CIGAR_STRING_INVALID_PRESENCE

        public static final SAMValidationError.Type MATE_CIGAR_STRING_INVALID_PRESENCE
        There is a Cigar String (stored in the MC Tag) for a read whose mate is NOT mapped.
      • INVALID_UNPAIRED_MATE_REFERENCE

        public static final SAMValidationError.Type INVALID_UNPAIRED_MATE_REFERENCE
        The mate reference of the unpaired read should be "*"
      • INVALID_UNALIGNED_MATE_START

        public static final SAMValidationError.Type INVALID_UNALIGNED_MATE_START
        The unaligned mate read start position should be 0
      • MISMATCH_CIGAR_SEQ_LENGTH

        public static final SAMValidationError.Type MISMATCH_CIGAR_SEQ_LENGTH
        Mismatch between the number of bases covered by the CIGAR and sequence
      • MISMATCH_SEQ_QUAL_LENGTH

        public static final SAMValidationError.Type MISMATCH_SEQ_QUAL_LENGTH
        Mismatch between the sequence and quality length
      • MISMATCH_FILE_SEQ_DICT

        public static final SAMValidationError.Type MISMATCH_FILE_SEQ_DICT
        Mismatch between file and sequence dictionaries
      • QUALITY_NOT_STORED

        public static final SAMValidationError.Type QUALITY_NOT_STORED
        Base quality is not stored for the read.
      • DUPLICATE_SAM_TAG

        public static final SAMValidationError.Type DUPLICATE_SAM_TAG
        A duplicate Sam tag was found in a record.
      • CG_TAG_FOUND_IN_ATTRIBUTES

        public static final SAMValidationError.Type CG_TAG_FOUND_IN_ATTRIBUTES
        The CG Tag should only be used in BAM format to hold a large cigar
    • Method Detail

      • values

        public static SAMValidationError.Type[] values()
        Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
        for (SAMValidationError.Type c : SAMValidationError.Type.values())
            System.out.println(c);
        
        Returns:
        an array containing the constants of this enum type, in the order they are declared
      • valueOf

        public static SAMValidationError.Type valueOf​(String name)
        Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
        Parameters:
        name - the name of the enum constant to be returned.
        Returns:
        the enum constant with the specified name
        Throws:
        IllegalArgumentException - if this enum type has no constant with the specified name
        NullPointerException - if the argument is null
      • getHistogramString

        public String getHistogramString()
        Returns:
        Format for writing to histogram summary output.