Struct bam::record::Flag

pub struct Flag(pub u16);

A wrapper around BAM/SAM flag.

You can check flag as record.flag().is_paired() or record.flag().0 | IS_PAIRED == 0. You can also modify the flag as record.flag_mut().set_paired(true) or record.flag_mut().0 |= IS_PAIRED.

Methods

impl Flag

pub fn is_paired(&self) -> bool

pub fn all_segments_aligned(&self) -> bool

pub fn is_mapped(&self) -> bool

pub fn mate_is_mapped(&self) -> bool

pub fn is_reverse_strand(&self) -> bool

pub fn mate_is_reverse_strand(&self) -> bool

pub fn first_in_pair(&self) -> bool

pub fn last_in_pair(&self) -> bool

pub fn is_secondary(&self) -> bool

pub fn fails_quality_controls(&self) -> bool

Returns true if the record fails filters, such as platform/vendor quality controls.

pub fn is_duplicate(&self) -> bool

Returns true if the record is PCR or optical duplicate.

pub fn is_supplementary(&self) -> bool

pub fn set_paired(&mut self, paired: bool)

Modifies the record flag. This function does not do any checks.

pub fn set_all_segments_aligned(&mut self, all_segments_aligned: bool)

Modifies the record flag. This function does not do any checks.

pub fn set_mapped(&mut self, mapped: bool)

Modifies the record flag. This function does not do any checks.

pub fn set_mate_mapped(&mut self, mate_mapped: bool)

Modifies the record flag. This function does not do any checks and does not modify the mate record.

pub fn set_strand(&mut self, forward_strand: bool)

Sets the record strand. Use true to set to forward strand, and false for the reverse strand.

pub fn set_mate_strand(&mut self, forward_strand: bool)

Sets the strand of the mate. Use true to set to forward strand, and false for the reverse strand. This function does not do any checks and does not modify the mate record.

pub fn set_first_in_pair(&mut self, is_first: bool)

Modifies the record flag. This function does not do any checks.

Use true to set the flag bit and false to unset.

pub fn set_last_in_pair(&mut self, is_last: bool)

Modifies the record flag. This function does not do any checks.

Use true to set the flag bit and false to unset.

pub fn set_secondary(&mut self, is_secondary: bool)

Modifies the record flag. This function does not do any checks.

Use true to set the flag bit and false to unset.

pub fn make_fail_quality_controls(&mut self, fails: bool)

Sets the record flag to fail or pass filters, such as platform/vendor quality controls.

Use true to set the flag bit and false to unset.

pub fn set_duplicate(&mut self, is_duplicate: bool)

Sets the record as PCR or optical duplicate.

pub fn set_supplementary(&mut self, is_supplementary: bool)

Trait Implementations

impl Clone for Flag

fn clone(&self) -> Flag

Returns a copy of the value.

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

Performs copy-assignment from source.

impl Copy for Flag

impl Debug for Flag

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

Formats the value using the given formatter.