Serializable
, Comparable<SAMValidationError.Type>
public static enum SAMValidationError.Type extends Enum<SAMValidationError.Type>
Enum Constant | Description |
---|---|
ADJACENT_INDEL_IN_CIGAR |
CIGAR string contains I followed by D, or vice versa
|
BAM_FILE_MISSING_TERMINATOR_BLOCK |
BAM appears to be healthy, but is an older file so doesn't have terminator block.
|
CIGAR_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 once
|
DUPLICATE_READ_GROUP_ID |
Same read group id appears more than once
|
E2_BASE_EQUALS_PRIMARY_BASE |
Secondary base calls should not be the same as primary, unless one or the other is N
|
EMPTY_READ |
|
HEADER_RECORD_MISSING_REQUIRED_TAG |
|
HEADER_TAG_MULTIPLY_DEFINED |
Header tag appears more than once in header line with different value
|
HEADER_TAG_NON_CONFORMING_VALUE |
Header tag contains illegal value
|
INVALID_ALIGNMENT_START |
alignment start is can not be correct
|
INVALID_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-8601
|
INVALID_FLAG_FIRST_OF_PAIR |
first of pair flag set for unpaired read
|
INVALID_FLAG_MATE_NEG_STRAND |
mate negative strand flag set for unpaired read
|
INVALID_FLAG_MATE_UNMAPPED |
mate unmapped flag set when mate is mapped or not set when mate is not mapped
|
INVALID_FLAG_NOT_PRIM_ALIGNMENT |
not primary alignment flag set for unmapped read
|
INVALID_FLAG_PROPER_PAIR |
proper pair flag set for unpaired read
|
INVALID_FLAG_READ_UNMAPPED |
mapped read flat not set for mapped read
|
INVALID_FLAG_SECOND_OF_PAIR |
second of pair flag set for unpaired read
|
INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT |
supplementary alignment flag set for unmapped read
|
INVALID_INDEX_FILE_POINTER |
Invalid virtualFilePointer in index
|
INVALID_INDEXING_BIN |
Indexing bin set on SAMRecord does not agree with computed value.
|
INVALID_INSERT_SIZE |
inferred insert size is out of range
|
INVALID_MAPPING_QUALITY |
mapping quality set for unmapped read or is >= 256
|
INVALID_MATE_REF_INDEX |
mate reference index (MRNM) set for unpaired read
|
INVALID_PLATFORM_VALUE |
The read group has an invalid value set for its PL field
|
INVALID_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 expected
|
INVALID_REFERENCE_INDEX |
reference index not found in sequence dictionary
|
INVALID_TAG_NM |
the NM tag (nucleotide differences) is incorrect
|
INVALID_UNALIGNED_MATE_START |
The unaligned mate read start position should be 0
|
INVALID_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 mate
|
MATE_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 sequence
|
MISMATCH_FILE_SEQ_DICT |
Mismatch between file and sequence dictionaries
|
MISMATCH_FLAG_MATE_NEG_STRAND |
mate negative strand flag does not match read negative strand flag of mate
|
MISMATCH_FLAG_MATE_UNMAPPED |
mate unmapped flag does not match read unmapped flag of mate
|
MISMATCH_MATE_ALIGNMENT_START |
mate alignment does not match alignment start of mate
|
MISMATCH_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 mate
|
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_QUALS_LENGTH |
|
MISMATCH_READ_LENGTH_AND_U2_LENGTH |
|
MISMATCH_SEQ_QUAL_LENGTH |
Mismatch between the sequence and quality length
|
MISSING_HEADER |
the sam/bam file is missing the header
|
MISSING_PLATFORM_VALUE |
The read group is missing its PL (platform unit) field
|
MISSING_READ_GROUP |
the header is missing read group information
|
MISSING_SEQUENCE_DICTIONARY |
there is no sequence dictionary in the header
|
MISSING_TAG_NM |
the NM tag (nucleotide differences) is missing
|
MISSING_VERSION_NUMBER |
|
PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND |
pair flag set but not marked as first or second of pair
|
POORLY_FORMATTED_HEADER_TAG |
Header tag does not have colon
|
QUALITY_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 header
|
RECORD_MISSING_READ_GROUP |
A SAMRecord is found with no read group id
|
RECORD_OUT_OF_ORDER |
the record is out of order
|
TAG_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
|
Modifier and Type | Field | Description |
---|---|---|
SAMValidationError.Severity |
severity |
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.
|
public static final SAMValidationError.Type INVALID_QUALITY_FORMAT
public static final SAMValidationError.Type INVALID_FLAG_PROPER_PAIR
public static final SAMValidationError.Type INVALID_FLAG_MATE_UNMAPPED
public static final SAMValidationError.Type MISMATCH_FLAG_MATE_UNMAPPED
public static final SAMValidationError.Type INVALID_FLAG_MATE_NEG_STRAND
public static final SAMValidationError.Type MISMATCH_FLAG_MATE_NEG_STRAND
public static final SAMValidationError.Type INVALID_FLAG_FIRST_OF_PAIR
public static final SAMValidationError.Type INVALID_FLAG_SECOND_OF_PAIR
public static final SAMValidationError.Type PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND
public static final SAMValidationError.Type INVALID_FLAG_NOT_PRIM_ALIGNMENT
public static final SAMValidationError.Type INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT
public static final SAMValidationError.Type INVALID_FLAG_READ_UNMAPPED
public static final SAMValidationError.Type INVALID_INSERT_SIZE
SAMRecord.MAX_INSERT_SIZE
public static final SAMValidationError.Type INVALID_MAPPING_QUALITY
public static final SAMValidationError.Type INVALID_CIGAR
public static final SAMValidationError.Type ADJACENT_INDEL_IN_CIGAR
public static final SAMValidationError.Type INVALID_MATE_REF_INDEX
public static final SAMValidationError.Type MISMATCH_MATE_REF_INDEX
public static final SAMValidationError.Type INVALID_REFERENCE_INDEX
public static final SAMValidationError.Type INVALID_ALIGNMENT_START
public static final SAMValidationError.Type MISMATCH_MATE_ALIGNMENT_START
public static final SAMValidationError.Type MATE_FIELD_MISMATCH
public static final SAMValidationError.Type INVALID_TAG_NM
public static final SAMValidationError.Type MISSING_TAG_NM
public static final SAMValidationError.Type MISSING_HEADER
public static final SAMValidationError.Type MISSING_SEQUENCE_DICTIONARY
public static final SAMValidationError.Type MISSING_READ_GROUP
public static final SAMValidationError.Type RECORD_OUT_OF_ORDER
public static final SAMValidationError.Type READ_GROUP_NOT_FOUND
public static final SAMValidationError.Type RECORD_MISSING_READ_GROUP
public static final SAMValidationError.Type INVALID_INDEXING_BIN
public static final SAMValidationError.Type MISSING_VERSION_NUMBER
public static final SAMValidationError.Type INVALID_VERSION_NUMBER
public static final SAMValidationError.Type TRUNCATED_FILE
public static final SAMValidationError.Type MISMATCH_READ_LENGTH_AND_QUALS_LENGTH
public static final SAMValidationError.Type EMPTY_READ
public static final SAMValidationError.Type CIGAR_MAPS_OFF_REFERENCE
public static final SAMValidationError.Type MISMATCH_READ_LENGTH_AND_E2_LENGTH
public static final SAMValidationError.Type MISMATCH_READ_LENGTH_AND_U2_LENGTH
public static final SAMValidationError.Type E2_BASE_EQUALS_PRIMARY_BASE
public static final SAMValidationError.Type BAM_FILE_MISSING_TERMINATOR_BLOCK
public static final SAMValidationError.Type UNRECOGNIZED_HEADER_TYPE
public static final SAMValidationError.Type POORLY_FORMATTED_HEADER_TAG
public static final SAMValidationError.Type HEADER_TAG_MULTIPLY_DEFINED
public static final SAMValidationError.Type HEADER_RECORD_MISSING_REQUIRED_TAG
public static final SAMValidationError.Type HEADER_TAG_NON_CONFORMING_VALUE
public static final SAMValidationError.Type INVALID_DATE_STRING
public static final SAMValidationError.Type TAG_VALUE_TOO_LARGE
public static final SAMValidationError.Type INVALID_INDEX_FILE_POINTER
public static final SAMValidationError.Type INVALID_PREDICTED_MEDIAN_INSERT_SIZE
public static final SAMValidationError.Type DUPLICATE_READ_GROUP_ID
public static final SAMValidationError.Type MISSING_PLATFORM_VALUE
public static final SAMValidationError.Type INVALID_PLATFORM_VALUE
public static final SAMValidationError.Type DUPLICATE_PROGRAM_GROUP_ID
public static final SAMValidationError.Type MATE_NOT_FOUND
public static final SAMValidationError.Type MATES_ARE_SAME_END
public static final SAMValidationError.Type MISMATCH_MATE_CIGAR_STRING
public static final SAMValidationError.Type MATE_CIGAR_STRING_INVALID_PRESENCE
public static final SAMValidationError.Type INVALID_UNPAIRED_MATE_REFERENCE
public static final SAMValidationError.Type INVALID_UNALIGNED_MATE_START
public static final SAMValidationError.Type MISMATCH_CIGAR_SEQ_LENGTH
public static final SAMValidationError.Type MISMATCH_SEQ_QUAL_LENGTH
public static final SAMValidationError.Type MISMATCH_FILE_SEQ_DICT
public static final SAMValidationError.Type QUALITY_NOT_STORED
public final SAMValidationError.Severity severity
public static SAMValidationError.Type[] values()
for (SAMValidationError.Type c : SAMValidationError.Type.values()) System.out.println(c);
public static SAMValidationError.Type valueOf(String name)
name
- the name of the enum constant to be returned.IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is nullpublic String getHistogramString()