Package htsjdk.samtools

Enum Class SAMValidationError.Type

java.lang.Object
java.lang.Enum<SAMValidationError.Type>
htsjdk.samtools.SAMValidationError.Type
All Implemented Interfaces:
Serializable, Comparable<SAMValidationError.Type>, Constable
Enclosing class:
SAMValidationError
public static enum SAMValidationError.Type extends Enum<SAMValidationError.Type>

  • Enum Constant Details

    • 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 flag not set for mapped read

    • INVALID_INSERT_SIZE

      public static final SAMValidationError.Type INVALID_INSERT_SIZE
      inferred insert size is out of range
      See Also:

    • 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

    • RECORD_OUT_OF_ORDER

      public static final SAMValidationError.Type RECORD_OUT_OF_ORDER
      the record is out of order

    • 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.

    • MISSING_VERSION_NUMBER

      public static final SAMValidationError.Type MISSING_VERSION_NUMBER

    • INVALID_VERSION_NUMBER

      public static final SAMValidationError.Type INVALID_VERSION_NUMBER

    • TRUNCATED_FILE

      public static final SAMValidationError.Type TRUNCATED_FILE

    • MISMATCH_READ_LENGTH_AND_QUALS_LENGTH

      public static final SAMValidationError.Type MISMATCH_READ_LENGTH_AND_QUALS_LENGTH

    • EMPTY_READ

      public static final SAMValidationError.Type EMPTY_READ

    • 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

    • INVALID_DATE_STRING

      public static final SAMValidationError.Type INVALID_DATE_STRING
      Date string is not ISO-8601

    • 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

    • REF_SEQ_TOO_LONG_FOR_BAI

      public static final SAMValidationError.Type REF_SEQ_TOO_LONG_FOR_BAI
      One or more reference sequences in the dictionary are too long for BAI indexing.

    • HEADER_TAG_INVALID_KEY

      public static final SAMValidationError.Type HEADER_TAG_INVALID_KEY
      Header tag key contains invalid characters or is not length two

  • Field Details

  • Method Details

    • values

      public static SAMValidationError.Type[] values()
      Returns an array containing the constants of this enum class, in the order they are declared.
      Returns:
      an array containing the constants of this enum class, in the order they are declared

    • valueOf

      public static SAMValidationError.Type valueOf(String name)
      Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (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 class 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.