ReadGroupInfo¶
#include <pbbam/ReadGroupInfo.h>
-
enum
PacBio::BAM::
BaseFeature
¶ This enum describes the base features that may be present in a read group’s records.
This information is stored in its description (@RG:DS).
Values:
-
DELETION_QV
¶
-
DELETION_TAG
¶
-
INSERTION_QV
¶
-
MERGE_QV
¶
-
SUBSTITUTION_QV
¶
-
SUBSTITUTION_TAG
¶
-
IPD
¶
-
PULSE_WIDTH
¶
-
PKMID
¶
-
PKMEAN
¶
-
PKMID2
¶
-
PKMEAN2
¶
-
LABEL
¶
-
LABEL_QV
¶
-
ALT_LABEL
¶
-
ALT_LABEL_QV
¶
-
PULSE_MERGE_QV
¶
-
PULSE_CALL
¶
-
PRE_PULSE_FRAMES
¶
-
PULSE_CALL_WIDTH
¶
-
START_FRAME
¶
-
PULSE_EXCLUSION
¶
-
-
enum
PacBio::BAM::
FrameCodec
¶ This enum describes the encoding types used for frame data within a read group’s records.
This information is stored in its description (@RG:DS).
Values:
-
RAW
¶
-
V1
¶
-
-
enum
PacBio::BAM::
BarcodeModeType
¶ This enum describes the experimental design of the barcodes within a read group’s records.
This information is stored in its description (@RG:DS).
Values:
-
NONE
¶
-
SYMMETRIC
¶
-
ASYMMETRIC
¶
-
TAILED
¶
-
-
enum
PacBio::BAM::
BarcodeQualityType
¶ This enum describes the type of value encoded by barcode quality, within a read group’s records.
This information is stored in its description (@RG:DS).
Values:
-
NONE
-
SCORE
¶
-
PROBABILITY
¶
-
-
class
PacBio::BAM::
ReadGroupInfo
¶ The ReadGroupInfo class represents a read group entry (@RG) in the SAM header.
Conversion & Validation
-
static ReadGroupInfo
FromSam
(const std::string &sam)¶ Creates a ReadGroupInfo object from SAM-formatted text.
- Return
- read group info object
- Parameters
sam
: SAM-formatted text
-
static std::string
ToSam
(const ReadGroupInfo &rg)¶ Converts a ReadGroupInfo object to its SAM-formatted text.
- Return
- SAM-formatted text (no trailing newline)
- Parameters
rg
: input ReadGroupInfo object
-
static int32_t
IdToInt
(const std::string &rgId)¶ Converts a read group ID (string) to its numeric value.
- Return
- numeric value of ID
- Parameters
rgId
: read group ID string
-
static std::string
IntToId
(const int32_t id)¶ Converts a read group ID number to its string representation.
- Return
- hexadecimal string representation of ID
- Parameters
id
: read group ID number
-
static std::string
SequencingChemistryFromTriple
(const std::string &bindingKit, const std::string &sequencingKit, const std::string &basecallerVersion)¶ - Return
- sequencing chemistry from (bindingKig, sequencingKit, basecallerVersion)
-
bool
IsValid
() const¶ Currently this checks to see that ReadGroupInfo::Id does not contain an empty string.
- Return
- true if read group info is valid
-
std::string
ToSam
() const¶ Converts this object to its SAM-formatted text.
- Return
- SAM-formatted text (no trailing newline)
Constructors & Related Methods
-
ReadGroupInfo
()¶ Creates an empty read group info object.
-
ReadGroupInfo
(std::string id)¶ Creates a read group info object with an ID.
- Parameters
id
: string representation of read group ID
-
ReadGroupInfo
(std::string movieName, std::string readType)¶ Creates a read group info object from a movie name & read type.
- See
- RecordType
- Parameters
movieName
: sequencing movie namereadType
: string version of record type
-
ReadGroupInfo
(std::string movieName, std::string readType, const PlatformModelType platform)¶ Creates a read group info object from a movie name, read type, and platform model.
- See
- RecordType
- Parameters
movieName
: sequencing movie namereadType
: string version of record typeplatform
: platform model type
-
ReadGroupInfo
(const ReadGroupInfo&)¶
-
ReadGroupInfo
(ReadGroupInfo&&)¶
-
ReadGroupInfo &
operator=
(const ReadGroupInfo&)¶
-
ReadGroupInfo &
operator=
(ReadGroupInfo&&)¶
-
~ReadGroupInfo
()¶
Comparison Operators
-
bool
operator==
(const ReadGroupInfo &other) const¶
Attributes
-
size_t
BarcodeCount
() const¶ - Return
- the number of barcode sequences in BarcodeFile
- Exceptions
std::runtime_error
: if barcode data not set. Check HasBarcodeData if this data may be absent.
-
std::string
BarcodeFile
() const¶ - Return
- name of FASTA file containing barcode sequences
- Exceptions
std::runtime_error
: if barcode data not set. Check HasBarcodeData if this data may be absent.
-
std::string
BarcodeHash
() const¶ - Return
- MD5 hash of the contents of BarcodeFile
- Exceptions
std::runtime_error
: if barcode data not set. Check HasBarcodeData if this data may be absent.
-
BarcodeModeType
BarcodeMode
() const¶ - Return
- experimental design type of barcodes
- Exceptions
std::runtime_error
: if barcode data not set. Check HasBarcodeData if this data may be absent.
-
BarcodeQualityType
BarcodeQuality
() const¶ - Return
- type of value encoded in the ‘bq’ tag
- Exceptions
std::runtime_error
: if barcode data is not set. Check HasBarcodeData if this data may be absent.
-
std::string
BasecallerVersion
() const¶ - Return
- basecaller version number (e.g. “2.1”)
-
std::string
BaseFeatureTag
(const BaseFeature &feature) const¶ - Return
- tag name in use for the specified for base feature
-
std::string
BindingKit
() const¶ - Return
- binding kit part number (e.g. “100236500”)
-
bool
Control
() const¶ - Return
- true if reads are classified as spike-in controls
-
std::map<std::string, std::string>
CustomTags
() const¶ Result map consists of {tagName => value}.
- Return
- any non-standard tags added to the @PG entry
-
std::string
Date
() const¶ - Return
- string value of @RG:DT
-
std::string
FlowOrder
() const¶ - Return
- string value of @RG:FO
-
std::string
FrameRateHz
() const¶ - Return
- frame rate in Hz
-
bool
HasBarcodeData
() const¶ - Return
- true if read group has barcode data
-
bool
HasBaseFeature
(const BaseFeature &feature) const¶ - Return
- true if read group has an entry for the specified base feature
-
std::string
Id
() const¶ - Return
- string value of @RG:ID
-
FrameCodec
IpdCodec
() const¶ - Return
- codec type in use for IPD
-
std::string
KeySequence
() const¶ - Return
- string value of @RG:KS
-
std::string
Library
() const¶ - Return
- string value of @RG:LB
-
std::string
MovieName
() const¶ - Return
- movie name (stored in @RG:PU)
-
std::string
Platform
() const¶ - Return
- string value of @RG:PL
-
PlatformModelType
PlatformModel
() const¶ - Return
- string value of @RG:PM
-
std::string
PredictedInsertSize
() const¶ - Return
- string value of @RG:PI
-
std::string
Programs
() const¶ - Return
- string value of @RG:PG
-
FrameCodec
PulseWidthCodec
() const¶ - Return
- codec type in use for PulseWidth
-
std::string
ReadType
() const¶ - Return
- string value of read type
-
std::string
Sample
() const¶ - Return
- string value of @RG:SM
-
std::string
SequencingCenter
() const¶ - Return
- string value of @RG:CN
-
std::string
SequencingChemistry
() const¶ - Return
- sequencing chemistry name
-
std::string
SequencingKit
() const¶ - Return
- sequencing kit part number
-
ReadGroupInfo &
BarcodeData
(const std::string &barcodeFile, const std::string &barcodeHash, size_t barcodeCount, BarcodeModeType barcodeMode, BarcodeQualityType barcodeQuality)¶ Sets read group’s barcode data.
Barcode fields are either absent or all must be present.
- See
- BarcodeFile BarcodeHash BarcodeCount BarcodeMode BarcodeQuality ReadGroupInfo::ClearBarcodeData
- Return
- reference to this object
- Parameters
barcodeFile
: barcode filenamebarcodeHash
: MD5 hash of barcode filebarcodeCount
: number of records in barcode filebarcodeMode
: experimental design of barcodesbarcodeQuality
: type of barcode quality value
-
ReadGroupInfo &
BasecallerVersion
(const std::string &versionNumber)¶ Sets the basecaller version number.
- Return
- reference to this object
- Parameters
versionNumber
: new value
-
ReadGroupInfo &
BaseFeatureTag
(const BaseFeature &feature, const std::string &tag)¶ Sets the tag to be used for a particular base feature.
- Return
- reference to this object
- Parameters
feature
: feature type begin updatedtag
: new value
-
ReadGroupInfo &
BindingKit
(const std::string &kitNumber)¶ Sets the binding kit part number.
- Return
- reference to this object
- Parameters
kitNumber
: new value
-
ReadGroupInfo &
ClearBarcodeData
()¶ Removes all barcode data from this read group.
- Return
- reference to this read group
-
ReadGroupInfo &
ClearBaseFeatures
()¶ Removes all base features from this read group.
- Return
- reference to this read group
-
ReadGroupInfo &
Control
(const bool ctrl)¶ Sets whether read group’s records are classifed as spike-in controls.
- Return
- reference to this object
- Parameters
ctrl
: true if records are spike-in controls
-
ReadGroupInfo &
CustomTags
(const std::map<std::string, std::string> &custom)¶ Sets a new collection of non-standard tags.
Custom tag map entries should consist of {tagName => value}.
- Return
- reference to this object
- Parameters
custom
: new tags
-
ReadGroupInfo &
Date
(const std::string &date)¶ Sets the value for @RG:DT.
- Return
- reference to this object
- Parameters
date
: new value
-
ReadGroupInfo &
FlowOrder
(const std::string &order)¶ Sets the value for @RG:FO.
- Return
- reference to this object
- Parameters
order
: new value
-
ReadGroupInfo &
FrameRateHz
(const std::string &frameRateHz)¶ Sets the frame rate.
- Return
- reference to this object
- Parameters
frameRateHz
: string value of frame rate in Hz
-
ReadGroupInfo &
Id
(const std::string &id)¶ Sets the read group’s ID.
- Return
- reference to this object
- Parameters
id
: string value of ID
-
ReadGroupInfo &
Id
(const std::string &movieName, const std::string &readType)¶ Sets the read group’s ID, from movie name & read type.
- Return
- reference to this object
- Parameters
movieName
: sequencing movie namereadType
: string version of read type
-
ReadGroupInfo &
IpdCodec
(const FrameCodec &codec, const std::string &tag = std::string())¶ Sets the codec type used for IPD.
- Return
- reference to this object
- Parameters
codec
: codec typetag
: IPD tag
-
ReadGroupInfo &
KeySequence
(const std::string &sequence)¶ Sets the value for @RG:KS.
- Return
- reference to this object
- Parameters
sequence
: new value
-
ReadGroupInfo &
Library
(const std::string &library)¶ Sets the value for @RG:LB.
- Return
- reference to this object
- Parameters
library
: new value
-
ReadGroupInfo &
MovieName
(const std::string &movieName)¶ Sets the value for movie name (stored in @RG:PU).
- Return
- reference to this object
- Parameters
movieName
: new value
-
ReadGroupInfo &
PredictedInsertSize
(const std::string &size)¶ Sets the value for @RG:PI.
- Return
- reference to this object
- Parameters
size
: new value
-
ReadGroupInfo &
Programs
(const std::string &programs)¶ Sets the value for @RG:PG.
- Return
- reference to this object
- Parameters
programs
: new value
-
ReadGroupInfo &
PlatformModel
(const PlatformModelType &platform)¶ Sets the value for @RG:PM.
- Return
- reference to this object
- Parameters
platformModel
: new value
-
ReadGroupInfo &
PulseWidthCodec
(const FrameCodec &codec, const std::string &tag = std::string())¶ Sets the codec type used for PulseWidth.
- Return
- reference to this object
- Parameters
codec
: codec typetag
: pulse width tag
-
ReadGroupInfo &
ReadType
(const std::string &type)¶ Sets the read type.
- Return
- reference to this object
- Parameters
type
: new value
-
ReadGroupInfo &
RemoveBaseFeature
(const BaseFeature &feature)¶ Removes a particular base feature from this read group.
- Return
- reference to this object
- Parameters
feature
: feature to remove
-
ReadGroupInfo &
Sample
(const std::string &sample)¶ Sets the value for @RG:SM.
- Return
- reference to this object
- Parameters
sample
: new value
-
ReadGroupInfo &
SequencingCenter
(const std::string ¢er)¶ Sets the value for @RG:CN.
- Return
- reference to this object
- Parameters
center
: new value
-
ReadGroupInfo &
SequencingKit
(const std::string &kitNumber)¶ Sets the sequencing kit part number.
- Return
- reference to this object
- Parameters
kitNumber
: new value
-
static ReadGroupInfo
-
PBBAM_EXPORT std::string PacBio::BAM::MakeReadGroupId(const std::string & movieName, const std::string & readType)
Creates a read group ID from a movie name & read type.
- Return
- hexadecimal string read group ID
- Parameters
movieName
: sequencing movie namereadType
: string version of read type