htsjdk.samtools

Enum SAMValidationError.Type

java.lang.Object

java.lang.Enum<SAMValidationError.Type>

htsjdk.samtools.SAMValidationError.Type

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<SAMValidationError.Type>

Enclosing class:

SAMValidationError

public static enum SAMValidationError.Type
extends java.lang.Enum<SAMValidationError.Type>

Enum Constant Summary

Enum Constants

Enum Constant and 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
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_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_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
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
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

Field Summary

Fields

Modifier and Type	Field and Description
SAMValidationError.Severity	severity

Method Summary

Modifier and Type	Method and Description
java.lang.String	getHistogramString()
static SAMValidationError.Type	valueOf(java.lang.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.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

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_INSERT_SIZE

public static final SAMValidationError.Type INVALID_INSERT_SIZE

inferred insert size is out of range

See Also:

SAMRecord.MAX_INSERT_SIZE

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

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.

Field Detail

severity

public final SAMValidationError.Severity severity

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(java.lang.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:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null

getHistogramString

public java.lang.String getHistogramString()

Returns:

Format for writing to histogram summary output.