Struct noodles_bam::record::Record [−][src]
pub struct Record(_);
Expand description
A BAM record.
A BAM record encodes the same fields as a SAM record:
- reference sequence ID (
RNAME
equiv.), - position (
POS
), - mapping quality (
MAPQ
), - flags (
FLAG
), - mate reference sequence ID (
RNEXT
equiv.), - mate position (
PNEXT
), - template length (
TLEN
), - read name (
QNAME
), - CIGAR operations (
CIGAR
), - sequence (
SEQ
), - quality scores (
QUAL
), and - optional data fields.
Additionally, it encodes the BAM index bin (bin
).
A bam::Record
wraps a raw byte buffer, and the fields should be considered immutable.
Implementations
pub fn try_from_sam_record(
reference_sequences: &ReferenceSequences,
record: &Record
) -> Result<Self>
pub fn try_from_sam_record(
reference_sequences: &ReferenceSequences,
record: &Record
) -> Result<Self>
Converts a SAM record to a BAM record.
Examples
use noodles_bam as bam; use noodles_sam::{self as sam, header::ReferenceSequences}; let reference_sequences = ReferenceSequences::default(); let sam_record = sam::Record::default(); let record = bam::Record::try_from_sam_record(&reference_sequences, &sam_record)?; assert_eq!(record, bam::Record::default());
Converts this record to a SAM record.
Examples
use noodles_bam as bam; use noodles_sam as sam; let reference_sequences = sam::header::ReferenceSequences::default(); let record = bam::Record::default(); let sam_record = record.try_into_sam_record(&reference_sequences)?; assert_eq!(sam_record, sam::Record::default());
Returns the reference sequence ID of this record.
The reference sequence ID is the index of the associated reference sequence in the SAM header or BAM reference sequences.
Examples
use noodles_bam as bam; let record = bam::Record::default(); assert!(record.reference_sequence_id().is_none());
Returns the start position of this record.
Despite the BAM format using 0-based positions, this normalizes the value as a 1-based position.
Examples
use noodles_bam as bam; let record = bam::Record::default(); assert!(record.position().is_none());
Returns the mapping quality of this record.
Examples
use noodles_bam as bam; use noodles_sam as sam; let record = bam::Record::default(); assert!(record.mapping_quality().is_none());
Returns the index bin that includes this record.
Examples
use noodles_bam as bam; let record = bam::Record::default(); assert_eq!(record.bin(), 4680);
Returns the SAM flags of this record.
Examples
use noodles_bam as bam; use noodles_sam as sam; let record = bam::Record::default(); assert_eq!(record.flags(), sam::record::Flags::UNMAPPED);
Returns the reference sequence ID of the mate of this record.
The mate reference sequence ID is the index of the associated reference sequence in the SAM header or BAM reference sequences.
Examples
use noodles_bam as bam; let record = bam::Record::default(); assert!(record.mate_reference_sequence_id().is_none());
Returns the start position of the mate of this record.
Despite the BAM format using 0-based positions, this normalizes the value as a 1-based position.
Examples
use noodles_bam as bam; let record = bam::Record::default(); assert!(record.mate_position().is_none());
Returns the template length of this record.
Examples
use noodles_bam as bam; let record = bam::Record::default(); assert_eq!(record.template_length(), 0);
Returns the read name of this record.
This is also called the query name.
Examples
use noodles_bam as bam; let record = bam::Record::default(); assert_eq!(record.read_name()?.to_bytes(), b"*");
Returns the CIGAR operations that describe how the read was mapped.
Examples
use noodles_bam as bam; let record = bam::Record::default(); assert!(record.cigar().is_empty());
Returns the bases in the sequence of this record.
Examples
use noodles_bam as bam; let record = bam::Record::default(); assert!(record.sequence().is_empty());
Returns the quality score for each base in the sequence.
Examples
use noodles_bam as bam; let record = bam::Record::default(); assert!(record.quality_scores().is_empty());
Trait Implementations
Auto Trait Implementations
impl RefUnwindSafe for Record
impl UnwindSafe for Record
Blanket Implementations
Mutably borrows from an owned value. Read more
Compare self to key
and return true
if they are equal.