Package htsjdk.samtools
Enum SAMValidationError.Type
- java.lang.Object
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- java.lang.Enum<SAMValidationError.Type>
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- htsjdk.samtools.SAMValidationError.Type
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- All Implemented Interfaces:
Serializable
,Comparable<SAMValidationError.Type>
- Enclosing class:
- SAMValidationError
public static enum SAMValidationError.Type extends Enum<SAMValidationError.Type>
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Enum Constant Summary
Enum Constants Enum Constant Description ADJACENT_INDEL_IN_CIGAR
CIGAR string contains I followed by D, or vice versaBAM_FILE_MISSING_TERMINATOR_BLOCK
BAM appears to be healthy, but is an older file so doesn't have terminator block.CG_TAG_FOUND_IN_ATTRIBUTES
The CG Tag should only be used in BAM format to hold a large cigarCIGAR_MAPS_OFF_REFERENCE
Bases corresponding to M operator in CIGAR are beyond the end of the reference.DUPLICATE_PROGRAM_GROUP_ID
Same program group id appears more than onceDUPLICATE_READ_GROUP_ID
Same read group id appears more than onceDUPLICATE_SAM_TAG
A duplicate Sam tag was found in a record.E2_BASE_EQUALS_PRIMARY_BASE
Secondary base calls should not be the same as primary, unless one or the other is NEMPTY_READ
HEADER_RECORD_MISSING_REQUIRED_TAG
HEADER_TAG_MULTIPLY_DEFINED
Header tag appears more than once in header line with different valueHEADER_TAG_NON_CONFORMING_VALUE
Header tag contains illegal valueINVALID_ALIGNMENT_START
alignment start is can not be correctINVALID_CIGAR
CIGAR string is empty for mapped read or not empty of unmapped read, or other CIGAR badness.INVALID_DATE_STRING
Date string is not ISO-8601INVALID_FLAG_FIRST_OF_PAIR
first of pair flag set for unpaired readINVALID_FLAG_MATE_NEG_STRAND
mate negative strand flag set for unpaired readINVALID_FLAG_MATE_UNMAPPED
mate unmapped flag set when mate is mapped or not set when mate is not mappedINVALID_FLAG_NOT_PRIM_ALIGNMENT
not primary alignment flag set for unmapped readINVALID_FLAG_PROPER_PAIR
proper pair flag set for unpaired readINVALID_FLAG_READ_UNMAPPED
mapped read flat not set for mapped readINVALID_FLAG_SECOND_OF_PAIR
second of pair flag set for unpaired readINVALID_FLAG_SUPPLEMENTARY_ALIGNMENT
supplementary alignment flag set for unmapped readINVALID_INDEX_FILE_POINTER
Invalid virtualFilePointer in indexINVALID_INDEXING_BIN
Indexing bin set on SAMRecord does not agree with computed value.INVALID_INSERT_SIZE
inferred insert size is out of rangeINVALID_MAPPING_QUALITY
mapping quality set for unmapped read or is >= 256INVALID_MATE_REF_INDEX
mate reference index (MRNM) set for unpaired readINVALID_PLATFORM_VALUE
The read group has an invalid value set for its PL fieldINVALID_PREDICTED_MEDIAN_INSERT_SIZE
PI tag value is not numeric.INVALID_QUALITY_FORMAT
quality encodings out of range; appear to be Solexa or Illumina when Phread expectedINVALID_REFERENCE_INDEX
reference index not found in sequence dictionaryINVALID_TAG_NM
the NM tag (nucleotide differences) is incorrectINVALID_UNALIGNED_MATE_START
The unaligned mate read start position should be 0INVALID_UNPAIRED_MATE_REFERENCE
The mate reference of the unpaired read should be "*"INVALID_VERSION_NUMBER
MATE_CIGAR_STRING_INVALID_PRESENCE
There is a Cigar String (stored in the MC Tag) for a read whose mate is NOT mapped.MATE_FIELD_MISMATCH
the record's mate fields do not match the corresponding fields of the mateMATE_NOT_FOUND
Read is marked as paired, but its pair was not found.MATES_ARE_SAME_END
Both mates are marked as first of pair, or both mates are marked as second of pair.MISMATCH_CIGAR_SEQ_LENGTH
Mismatch between the number of bases covered by the CIGAR and sequenceMISMATCH_FILE_SEQ_DICT
Mismatch between file and sequence dictionariesMISMATCH_FLAG_MATE_NEG_STRAND
mate negative strand flag does not match read negative strand flag of mateMISMATCH_FLAG_MATE_UNMAPPED
mate unmapped flag does not match read unmapped flag of mateMISMATCH_MATE_ALIGNMENT_START
mate alignment does not match alignment start of mateMISMATCH_MATE_CIGAR_STRING
The Cigar String in the MC Tag does not match the Cigar String for the mate of this read.MISMATCH_MATE_REF_INDEX
mate reference index (MRNM) does not match reference index of mateMISMATCH_READ_LENGTH_AND_E2_LENGTH
Length of E2 (secondary base calls) and U2 (secondary base quals) tag values should match read lengthMISMATCH_READ_LENGTH_AND_QUALS_LENGTH
MISMATCH_READ_LENGTH_AND_U2_LENGTH
MISMATCH_SEQ_QUAL_LENGTH
Mismatch between the sequence and quality lengthMISSING_HEADER
the sam/bam file is missing the headerMISSING_PLATFORM_VALUE
The read group is missing its PL (platform unit) fieldMISSING_READ_GROUP
the header is missing read group informationMISSING_SEQUENCE_DICTIONARY
there is no sequence dictionary in the headerMISSING_TAG_NM
the NM tag (nucleotide differences) is missingMISSING_VERSION_NUMBER
PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND
pair flag set but not marked as first or second of pairPOORLY_FORMATTED_HEADER_TAG
Header tag does not have colonQUALITY_NOT_STORED
Base quality is not stored for the read.READ_GROUP_NOT_FOUND
A read group ID on a SAMRecord is not found in the headerRECORD_MISSING_READ_GROUP
A SAMRecord is found with no read group idRECORD_OUT_OF_ORDER
the record is out of orderTAG_VALUE_TOO_LARGE
Unsigned integer tag value is deprecated in BAM.TRUNCATED_FILE
UNRECOGNIZED_HEADER_TYPE
Header record is not one of the standard types
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Field Summary
Fields Modifier and Type Field Description SAMValidationError.Severity
severity
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description String
getHistogramString()
static SAMValidationError.Type
valueOf(String name)
Returns the enum constant of this type with the specified name.static SAMValidationError.Type[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
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Enum Constant Detail
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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
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INVALID_FLAG_PROPER_PAIR
public static final SAMValidationError.Type INVALID_FLAG_PROPER_PAIR
proper pair flag set for unpaired read
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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
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MISMATCH_FLAG_MATE_UNMAPPED
public static final SAMValidationError.Type MISMATCH_FLAG_MATE_UNMAPPED
mate unmapped flag does not match read unmapped flag of mate
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INVALID_FLAG_MATE_NEG_STRAND
public static final SAMValidationError.Type INVALID_FLAG_MATE_NEG_STRAND
mate negative strand flag set for unpaired read
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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
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INVALID_FLAG_FIRST_OF_PAIR
public static final SAMValidationError.Type INVALID_FLAG_FIRST_OF_PAIR
first of pair flag set for unpaired read
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INVALID_FLAG_SECOND_OF_PAIR
public static final SAMValidationError.Type INVALID_FLAG_SECOND_OF_PAIR
second of pair flag set for unpaired read
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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
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INVALID_FLAG_NOT_PRIM_ALIGNMENT
public static final SAMValidationError.Type INVALID_FLAG_NOT_PRIM_ALIGNMENT
not primary alignment flag set for unmapped read
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INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT
public static final SAMValidationError.Type INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT
supplementary alignment flag set for unmapped read
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INVALID_FLAG_READ_UNMAPPED
public static final SAMValidationError.Type INVALID_FLAG_READ_UNMAPPED
mapped read flat not set for mapped read
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INVALID_INSERT_SIZE
public static final SAMValidationError.Type INVALID_INSERT_SIZE
inferred insert size is out of range- See Also:
SAMRecord.MAX_INSERT_SIZE
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INVALID_MAPPING_QUALITY
public static final SAMValidationError.Type INVALID_MAPPING_QUALITY
mapping quality set for unmapped read or is >= 256
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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.
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ADJACENT_INDEL_IN_CIGAR
public static final SAMValidationError.Type ADJACENT_INDEL_IN_CIGAR
CIGAR string contains I followed by D, or vice versa
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INVALID_MATE_REF_INDEX
public static final SAMValidationError.Type INVALID_MATE_REF_INDEX
mate reference index (MRNM) set for unpaired read
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MISMATCH_MATE_REF_INDEX
public static final SAMValidationError.Type MISMATCH_MATE_REF_INDEX
mate reference index (MRNM) does not match reference index of mate
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INVALID_REFERENCE_INDEX
public static final SAMValidationError.Type INVALID_REFERENCE_INDEX
reference index not found in sequence dictionary
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INVALID_ALIGNMENT_START
public static final SAMValidationError.Type INVALID_ALIGNMENT_START
alignment start is can not be correct
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MISMATCH_MATE_ALIGNMENT_START
public static final SAMValidationError.Type MISMATCH_MATE_ALIGNMENT_START
mate alignment does not match alignment start of mate
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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
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INVALID_TAG_NM
public static final SAMValidationError.Type INVALID_TAG_NM
the NM tag (nucleotide differences) is incorrect
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MISSING_TAG_NM
public static final SAMValidationError.Type MISSING_TAG_NM
the NM tag (nucleotide differences) is missing
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MISSING_HEADER
public static final SAMValidationError.Type MISSING_HEADER
the sam/bam file is missing the header
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MISSING_SEQUENCE_DICTIONARY
public static final SAMValidationError.Type MISSING_SEQUENCE_DICTIONARY
there is no sequence dictionary in the header
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MISSING_READ_GROUP
public static final SAMValidationError.Type MISSING_READ_GROUP
the header is missing read group information
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RECORD_OUT_OF_ORDER
public static final SAMValidationError.Type RECORD_OUT_OF_ORDER
the record is out of order
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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
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RECORD_MISSING_READ_GROUP
public static final SAMValidationError.Type RECORD_MISSING_READ_GROUP
A SAMRecord is found with no read group id
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INVALID_INDEXING_BIN
public static final SAMValidationError.Type INVALID_INDEXING_BIN
Indexing bin set on SAMRecord does not agree with computed value.
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MISSING_VERSION_NUMBER
public static final SAMValidationError.Type MISSING_VERSION_NUMBER
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INVALID_VERSION_NUMBER
public static final SAMValidationError.Type INVALID_VERSION_NUMBER
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TRUNCATED_FILE
public static final SAMValidationError.Type TRUNCATED_FILE
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MISMATCH_READ_LENGTH_AND_QUALS_LENGTH
public static final SAMValidationError.Type MISMATCH_READ_LENGTH_AND_QUALS_LENGTH
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EMPTY_READ
public static final SAMValidationError.Type EMPTY_READ
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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.
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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
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MISMATCH_READ_LENGTH_AND_U2_LENGTH
public static final SAMValidationError.Type MISMATCH_READ_LENGTH_AND_U2_LENGTH
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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
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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.
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UNRECOGNIZED_HEADER_TYPE
public static final SAMValidationError.Type UNRECOGNIZED_HEADER_TYPE
Header record is not one of the standard types
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POORLY_FORMATTED_HEADER_TAG
public static final SAMValidationError.Type POORLY_FORMATTED_HEADER_TAG
Header tag does not have colon
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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
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HEADER_RECORD_MISSING_REQUIRED_TAG
public static final SAMValidationError.Type HEADER_RECORD_MISSING_REQUIRED_TAG
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HEADER_TAG_NON_CONFORMING_VALUE
public static final SAMValidationError.Type HEADER_TAG_NON_CONFORMING_VALUE
Header tag contains illegal value
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INVALID_DATE_STRING
public static final SAMValidationError.Type INVALID_DATE_STRING
Date string is not ISO-8601
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TAG_VALUE_TOO_LARGE
public static final SAMValidationError.Type TAG_VALUE_TOO_LARGE
Unsigned integer tag value is deprecated in BAM.
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INVALID_INDEX_FILE_POINTER
public static final SAMValidationError.Type INVALID_INDEX_FILE_POINTER
Invalid virtualFilePointer in index
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INVALID_PREDICTED_MEDIAN_INSERT_SIZE
public static final SAMValidationError.Type INVALID_PREDICTED_MEDIAN_INSERT_SIZE
PI tag value is not numeric.
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DUPLICATE_READ_GROUP_ID
public static final SAMValidationError.Type DUPLICATE_READ_GROUP_ID
Same read group id appears more than once
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MISSING_PLATFORM_VALUE
public static final SAMValidationError.Type MISSING_PLATFORM_VALUE
The read group is missing its PL (platform unit) field
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INVALID_PLATFORM_VALUE
public static final SAMValidationError.Type INVALID_PLATFORM_VALUE
The read group has an invalid value set for its PL field
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DUPLICATE_PROGRAM_GROUP_ID
public static final SAMValidationError.Type DUPLICATE_PROGRAM_GROUP_ID
Same program group id appears more than once
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MATE_NOT_FOUND
public static final SAMValidationError.Type MATE_NOT_FOUND
Read is marked as paired, but its pair was not found.
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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.
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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.
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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.
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INVALID_UNPAIRED_MATE_REFERENCE
public static final SAMValidationError.Type INVALID_UNPAIRED_MATE_REFERENCE
The mate reference of the unpaired read should be "*"
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INVALID_UNALIGNED_MATE_START
public static final SAMValidationError.Type INVALID_UNALIGNED_MATE_START
The unaligned mate read start position should be 0
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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
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MISMATCH_SEQ_QUAL_LENGTH
public static final SAMValidationError.Type MISMATCH_SEQ_QUAL_LENGTH
Mismatch between the sequence and quality length
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MISMATCH_FILE_SEQ_DICT
public static final SAMValidationError.Type MISMATCH_FILE_SEQ_DICT
Mismatch between file and sequence dictionaries
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QUALITY_NOT_STORED
public static final SAMValidationError.Type QUALITY_NOT_STORED
Base quality is not stored for the read.
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DUPLICATE_SAM_TAG
public static final SAMValidationError.Type DUPLICATE_SAM_TAG
A duplicate Sam tag was found in a record.
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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
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Field Detail
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severity
public final SAMValidationError.Severity severity
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Method Detail
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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
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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 nameNullPointerException
- if the argument is null
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getHistogramString
public String getHistogramString()
- Returns:
- Format for writing to histogram summary output.
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