Struct noodles_sam::alignment::record::Flags

pub struct Flags(/* private fields */);

Alignment record flags.

Implementations

impl Flags

pub const SEGMENTED: Self = _

Read is segmented (0x01).

pub const PROPERLY_ALIGNED: Self = _

👎Deprecated since 0.54.0: Use PROPERLY_SEGMENTED instead.

Each segment in the read is properly aligned (0x02).

pub const PROPERLY_SEGMENTED: Self = _

Each segment in the read is properly aligned (0x02).

pub const UNMAPPED: Self = _

Read is unmapped (Ox04).

pub const MATE_UNMAPPED: Self = _

The mate is unmapped (0x08).

pub const REVERSE_COMPLEMENTED: Self = _

The sequence is reverse complemented (0x10).

pub const MATE_REVERSE_COMPLEMENTED: Self = _

The sequence of the mate is reverse complemented (0x20).

pub const FIRST_SEGMENT: Self = _

First segment in the read (0x40).

pub const LAST_SEGMENT: Self = _

Last segment in the read (0x80).

pub const SECONDARY: Self = _

Secondary read (0x0100).

pub const QC_FAIL: Self = _

Read failed quality checks (0x0200).

pub const DUPLICATE: Self = _

PCR or optical duplicate read (0x0400).

pub const SUPPLEMENTARY: Self = _

Supplementary alignment (0x0800).

impl Flags

pub const fn empty() -> Self

Get a flags value with all bits unset.

pub const fn all() -> Self

Get a flags value with all known bits set.

pub const fn bits(&self) -> u16

Get the underlying bits value.

The returned value is exactly the bits set in this flags value.

pub const fn from_bits(bits: u16) -> Option<Self>

Convert from a bits value.

This method will return None if any unknown bits are set.

pub const fn from_bits_truncate(bits: u16) -> Self

Convert from a bits value, unsetting any unknown bits.

pub const fn from_bits_retain(bits: u16) -> Self

Convert from a bits value exactly.

pub fn from_name(name: &str) -> Option<Self>

Get a flags value with the bits of a flag with the given name set.

This method will return None if name is empty or doesn’t correspond to any named flag.

pub const fn is_empty(&self) -> bool

Whether all bits in this flags value are unset.

pub const fn is_all(&self) -> bool

Whether all known bits in this flags value are set.

pub const fn intersects(&self, other: Self) -> bool

Whether any set bits in a source flags value are also set in a target flags value.

pub const fn contains(&self, other: Self) -> bool

Whether all set bits in a source flags value are also set in a target flags value.

pub fn insert(&mut self, other: Self)

The bitwise or (|) of the bits in two flags values.

pub fn remove(&mut self, other: Self)

The intersection of a source flags value with the complement of a target flags value (&!).

This method is not equivalent to self & !other when other has unknown bits set. remove won’t truncate other, but the ! operator will.

pub fn toggle(&mut self, other: Self)

The bitwise exclusive-or (^) of the bits in two flags values.

pub fn set(&mut self, other: Self, value: bool)

Call insert when value is true or remove when value is false.

pub const fn intersection(self, other: Self) -> Self

The bitwise and (&) of the bits in two flags values.

pub const fn union(self, other: Self) -> Self

The bitwise or (|) of the bits in two flags values.

pub const fn difference(self, other: Self) -> Self

The intersection of a source flags value with the complement of a target flags value (&!).

This method is not equivalent to self & !other when other has unknown bits set. difference won’t truncate other, but the ! operator will.

pub const fn symmetric_difference(self, other: Self) -> Self

The bitwise exclusive-or (^) of the bits in two flags values.

pub const fn complement(self) -> Self

The bitwise negation (!) of the bits in a flags value, truncating the result.

impl Flags

pub const fn iter(&self) -> Iter<Flags>

Yield a set of contained flags values.

Each yielded flags value will correspond to a defined named flag. Any unknown bits will be yielded together as a final flags value.

pub const fn iter_names(&self) -> IterNames<Flags>

Yield a set of contained named flags values.

This method is like iter, except only yields bits in contained named flags. Any unknown bits, or bits not corresponding to a contained flag will not be yielded.

impl Flags

pub fn is_segmented(self) -> bool

Returns whether the SEGMENTED flag is set.

Examples

use noodles_sam::alignment::record::Flags;
assert!(Flags::SEGMENTED.is_segmented());
assert!(!Flags::UNMAPPED.is_segmented());

pub fn is_properly_aligned(self) -> bool

👎Deprecated since 0.54.0: Use Flags::is_properly_segmented instead.

Returns whether the PROPERLY_ALIGNED flag is set.

Examples

use noodles_sam::alignment::record::Flags;
assert!(Flags::PROPERLY_ALIGNED.is_properly_aligned());
assert!(!Flags::UNMAPPED.is_properly_aligned());

pub fn is_properly_segmented(self) -> bool

Returns whether the PROPERLY_SEGMENTED flag is set.

Examples

use noodles_sam::alignment::record::Flags;
assert!(Flags::PROPERLY_SEGMENTED.is_properly_segmented());
assert!(!Flags::UNMAPPED.is_properly_segmented());

pub fn is_unmapped(self) -> bool

Returns whether the UNMAPPED flag is set.

Examples

use noodles_sam::alignment::record::Flags;
assert!(Flags::UNMAPPED.is_unmapped());
assert!(!Flags::SEGMENTED.is_unmapped());

pub fn is_mate_unmapped(self) -> bool

Returns whether the MATE_UNMAPPED flag is set.

Examples

use noodles_sam::alignment::record::Flags;
assert!(Flags::MATE_UNMAPPED.is_mate_unmapped());
assert!(!Flags::UNMAPPED.is_mate_unmapped());

pub fn is_reverse_complemented(self) -> bool

Returns whether the REVERSE_COMPLEMENTED flag is set.

Examples

use noodles_sam::alignment::record::Flags;
assert!(Flags::REVERSE_COMPLEMENTED.is_reverse_complemented());
assert!(!Flags::UNMAPPED.is_reverse_complemented());

pub fn is_mate_reverse_complemented(self) -> bool

Returns whether the MATE_REVERSE_COMPLEMENTED flag is set.

Examples

use noodles_sam::alignment::record::Flags;
assert!(Flags::MATE_REVERSE_COMPLEMENTED.is_mate_reverse_complemented());
assert!(!Flags::UNMAPPED.is_mate_reverse_complemented());

pub fn is_first_segment(self) -> bool

Returns whether the FIRST_SEGMENT flag is set.

Examples

use noodles_sam::alignment::record::Flags;
assert!(Flags::FIRST_SEGMENT.is_first_segment());
assert!(!Flags::UNMAPPED.is_first_segment());

pub fn is_last_segment(self) -> bool

Returns whether the LAST_SEGMENT flag is set.

Examples

use noodles_sam::alignment::record::Flags;
assert!(Flags::LAST_SEGMENT.is_last_segment());
assert!(!Flags::UNMAPPED.is_last_segment());

pub fn is_secondary(self) -> bool

Returns whether the SECONDARY flag is set.

Examples

use noodles_sam::alignment::record::Flags;
assert!(Flags::SECONDARY.is_secondary());
assert!(!Flags::UNMAPPED.is_secondary());

pub fn is_qc_fail(self) -> bool

Returns whether the QC_FAIL flag is set.

Examples

use noodles_sam::alignment::record::Flags;
assert!(Flags::QC_FAIL.is_qc_fail());
assert!(!Flags::UNMAPPED.is_qc_fail());

pub fn is_duplicate(self) -> bool

Returns whether the DUPLICATE flag is set.

Examples

use noodles_sam::alignment::record::Flags;
assert!(Flags::DUPLICATE.is_duplicate());
assert!(!Flags::UNMAPPED.is_duplicate());

pub fn is_supplementary(self) -> bool

Returns whether the SUPPLEMENTARY flag is set.

Examples

use noodles_sam::alignment::record::Flags;
assert!(Flags::SUPPLEMENTARY.is_supplementary());
assert!(!Flags::UNMAPPED.is_supplementary());

Trait Implementations

impl Binary for Flags

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl BitAnd for Flags

fn bitand(self, other: Self) -> Self

The bitwise and (&) of the bits in two flags values.

type Output = Flags

The resulting type after applying the & operator.

impl BitAndAssign for Flags

fn bitand_assign(&mut self, other: Self)

The bitwise and (&) of the bits in two flags values.

impl BitOr for Flags

fn bitor(self, other: Flags) -> Self

The bitwise or (|) of the bits in two flags values.

type Output = Flags

The resulting type after applying the | operator.

impl BitOrAssign for Flags

fn bitor_assign(&mut self, other: Self)

The bitwise or (|) of the bits in two flags values.

impl BitXor for Flags

fn bitxor(self, other: Self) -> Self

The bitwise exclusive-or (^) of the bits in two flags values.

type Output = Flags

The resulting type after applying the ^ operator.

impl BitXorAssign for Flags

fn bitxor_assign(&mut self, other: Self)

The bitwise exclusive-or (^) of the bits in two flags values.

impl Clone for Flags

fn clone(&self) -> Flags

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Flags

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for Flags

fn default() -> Flags

Returns the “default value” for a type.

impl Extend<Flags> for Flags

fn extend<T: IntoIterator<Item = Self>>(&mut self, iterator: T)

The bitwise or (|) of the bits in each flags value.

fn extend_one(&mut self, item: A)

🔬This is a nightly-only experimental API. (extend_one)

Extends a collection with exactly one element.

fn extend_reserve(&mut self, additional: usize)

🔬This is a nightly-only experimental API. (extend_one)

Reserves capacity in a collection for the given number of additional elements.

impl Flags for Flags

const FLAGS: &'static [Flag<Flags>] = _

The set of defined flags.

type Bits = u16

The underlying bits type.

fn bits(&self) -> u16

Get the underlying bits value.

fn from_bits_retain(bits: u16) -> Flags

Convert from a bits value exactly.

fn empty() -> Self

Get a flags value with all bits unset.

fn all() -> Self

Get a flags value with all known bits set.

fn from_bits(bits: Self::Bits) -> Option<Self>

Convert from a bits value.

fn from_bits_truncate(bits: Self::Bits) -> Self

Convert from a bits value, unsetting any unknown bits.

fn from_name(name: &str) -> Option<Self>

Get a flags value with the bits of a flag with the given name set.

fn iter(&self) -> Iter<Self>

Yield a set of contained flags values.

fn iter_names(&self) -> IterNames<Self>

Yield a set of contained named flags values.

fn is_empty(&self) -> bool

Whether all bits in this flags value are unset.

fn is_all(&self) -> bool

Whether all known bits in this flags value are set.

fn intersects(&self, other: Self) -> bool

where Self: Sized,

Whether any set bits in a source flags value are also set in a target flags value.

fn contains(&self, other: Self) -> bool

where Self: Sized,

Whether all set bits in a source flags value are also set in a target flags value.

fn insert(&mut self, other: Self)

where Self: Sized,

The bitwise or (|) of the bits in two flags values.

fn remove(&mut self, other: Self)

where Self: Sized,

The intersection of a source flags value with the complement of a target flags value (&!).

fn toggle(&mut self, other: Self)

where Self: Sized,

The bitwise exclusive-or (^) of the bits in two flags values.

fn set(&mut self, other: Self, value: bool)

where Self: Sized,

Call Flags::insert when value is true or Flags::remove when value is false.

fn intersection(self, other: Self) -> Self

The bitwise and (&) of the bits in two flags values.

fn union(self, other: Self) -> Self

The bitwise or (|) of the bits in two flags values.

fn difference(self, other: Self) -> Self

The intersection of a source flags value with the complement of a target flags value (&!).

fn symmetric_difference(self, other: Self) -> Self

The bitwise exclusive-or (^) of the bits in two flags values.

fn complement(self) -> Self

The bitwise negation (!) of the bits in a flags value, truncating the result.

impl From<Flags> for u16

fn from(flags: Flags) -> Self

Converts to this type from the input type.

impl From<u16> for Flags

fn from(value: u16) -> Self

Converts to this type from the input type.

impl FromIterator<Flags> for Flags

fn from_iter<T: IntoIterator<Item = Self>>(iterator: T) -> Self

The bitwise or (|) of the bits in each flags value.

impl IntoIterator for Flags

type Item = Flags

The type of the elements being iterated over.

type IntoIter = Iter<Flags>

Which kind of iterator are we turning this into?

fn into_iter(self) -> Self::IntoIter

Creates an iterator from a value.

impl LowerHex for Flags

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Not for Flags

fn not(self) -> Self

The bitwise negation (!) of the bits in a flags value, truncating the result.

type Output = Flags

The resulting type after applying the ! operator.

impl Octal for Flags

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl PartialEq for Flags

fn eq(&self, other: &Flags) -> bool

This method tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PublicFlags for Flags

type Primitive = u16

The type of the underlying storage.

type Internal = InternalBitFlags

The type of the internal field on the generated flags type.

impl Sub for Flags

fn sub(self, other: Self) -> Self

The intersection of a source flags value with the complement of a target flags value (&!).

This method is not equivalent to self & !other when other has unknown bits set. difference won’t truncate other, but the ! operator will.

type Output = Flags

The resulting type after applying the - operator.

impl SubAssign for Flags

fn sub_assign(&mut self, other: Self)

The intersection of a source flags value with the complement of a target flags value (&!).

This method is not equivalent to self & !other when other has unknown bits set. difference won’t truncate other, but the ! operator will.

impl UpperHex for Flags

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Copy for Flags

impl Eq for Flags

impl StructuralPartialEq for Flags