Struct ObservedCombinations 

pub struct ObservedCombinations { /* private fields */ }

Container for ObservedCombination objects

The core is a HashMap of the ObservedRegions seen so far and a HashMap of ObservedCombination objects that link to the contained regions. An additional HashMap plus the library is added when library comparison is run. It also carries the region ids to be considered in order.

Implementations

impl ObservedCombinations

pub fn new(region_ids: Vec<String>, filter_config: FilterConfig) -> Self

pub fn merge( &mut self, new_counts: ObservedCombinations, ) -> Result<(), ReadCountError>

Merge counts from another ObservedCombinations object into this one

New counts and regions are added to this container with an empty return on successful operation and an error returned if the two ObservedCombinations objects are incompatible.

Reasons for incompatibility:

• Library comparison has occured
• Region ids are not the same

pub fn len(&self) -> usize

Number of distinct observed combination types

pub fn is_empty(&self) -> bool

Check if there are no observed combinations

pub fn total_filtered(&self) -> u64

Total number of filtered reads

pub fn add_or_increment_combination( &mut self, comb_key: &CombinationKey, group: ReadGroup, ) -> Result<(), Error>

Increment a combination count or add a new combination if it hasn’t been seen yet

pub fn update_filter_count(&mut self, read: &ReadPair, reason: FilterReason)

Update filter counts without checking the read

Passes through to self.filtered_reads.update_count, useful when using cached FilterReasons to prevent needing to re-align.

pub fn filter_readpair( &mut self, record: &ReadPair, increment: bool, ) -> Option<FilterReason>

Determine if a read should be filtered

Pass through to self.filtered_reads.filter_read, which Checks whether the read should be filtered, adding it to the appropriate count if increment is true, and returns a the filter reason.

pub fn filter_alignment( &mut self, record: &ReadPair, f_alignment: &Alignment, r_alignment: Option<&Alignment>, increment: bool, ) -> Option<FilterReason>

Determine if an alignment should be filtered

Passes through to self.filtered_reads.filter_alignment, which checks if an alignment should be filtered, adding it to the appropriate count if increment is true, and returns a the filter reason.

pub fn cache(&mut self, key: SeqPair, value: CacheHit)

Add a result to the cache

pub fn check_cache( &mut self, record: &ReadPair, increment: bool, ) -> Result<Option<CacheHit>, Error>

Check if a read is cached and optionally increment it

pub fn compare_to_library( &mut self, library: Library, progress_style: Option<&ProgressStyle>, distance_metric: DistanceMetric, max_matches: usize, threads: usize, ) -> Result<(), LibraryError>

Compare observed combinations to those expected in a Library

pub fn is_compared_to_library(&self) -> bool

Check if library comparison has occured

pub fn summarise(&self) -> ReadSummary

Summarise the observed read count categories

Counts the occurance of each CombinationMatch, so makes little sense if library comparison hasn’t occured first as it will just sum the total reads

pub fn write_tsv(&self, file: File, sort: bool) -> Result<(), Error>

Write all counts to file

pub fn write_summary_tsv(&self, file: File, sort: bool) -> Result<(), Error>

Write matched library combination counts to file

pub fn write_filtered_tsv(&self, file: File, sort: bool) -> Result<(), Error>

Write all counts to file

Trait Implementations

impl Debug for ObservedCombinations

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

Formats the value using the given formatter.