Struct InputBamBuilder 

pub struct InputBamBuilder { /* private fields */ }

Builder for InputBam.

Implementations

impl InputBamBuilder

pub fn bam_path(&mut self, value: PathOrURLOrStdin) -> &mut Self

Input BAM file. Set to a local file path, or set to - to read from stdin, or set to a URL to read from a remote file. If using stdin and piping in from samtools view, always include the header with the -h option.

pub fn min_seq_len<VALUE: Into<u64>>(&mut self, value: VALUE) -> &mut Self

Exclude reads whose sequence length in the BAM file is below this value. Defaults to 0.

pub fn min_align_len<VALUE: Into<i64>>(&mut self, value: VALUE) -> &mut Self

Exclude reads whose alignment length in the BAM file is below this value. Defaults to unused.

pub fn read_id<VALUE: Into<String>>(&mut self, value: VALUE) -> &mut Self

Only include this read id, defaults to unused i.e. all reads are used. NOTE: if there are multiple alignments corresponding to this read id, all of them are used.

pub fn read_id_list<VALUE: Into<String>>(&mut self, value: VALUE) -> &mut Self

Path to file containing list of read IDs (one per line). Lines starting with ‘#’ are treated as comments and ignored. Cannot be used together with –read-id.

pub fn read_id_set<VALUE: Into<HashSet<String>>>( &mut self, value: VALUE, ) -> &mut Self

Internal HashSet of read IDs loaded from read_id_list file. This is populated automatically and not exposed to users.

pub fn threads<VALUE: Into<NonZeroU32>>(&mut self, value: VALUE) -> &mut Self

Number of threads used during some aspects of program execution

pub fn include_zero_len(&mut self, value: bool) -> &mut Self

Include “zero-length” sequences e.g. sequences with “*” in the sequence field. By default, these sequences are excluded to avoid processing errors. If this flag is set, these reads are included irrespective of any minimum sequence or align length criteria the user may have set. WARNINGS: (1) Some functions of the codebase may break or produce incorrect results if you use this flag. (2) due to a technical reason, we need a DNA sequence in the sequence field and cannot infer sequence length from other sources e.g. CIGAR strings.

pub fn read_filter(&mut self, value: String) -> &mut Self

Only retain reads of this type. Allowed types are primary_forward, primary_reverse, secondary_forward, secondary_reverse, supplementary_forward, supplementary_reverse and unmapped. Specify more than one type if needed separated by commas, in which case reads of any type in list are retained. Defaults to retain reads of all types.

pub fn sample_fraction(&mut self, value: F32Bw0and1) -> &mut Self

Subsample BAM to retain only this fraction of total number of reads, defaults to 1.0. The sampling algorithm considers every read according to the specified probability, so due to this, you may not always get the same number of reads e.g. if you set -s 0.05 in a file with 1000 reads, you will get 50 +- sqrt(50) reads. NOTE: a new subsample is drawn every time as the seed is not fixed. If you want reproducibility, consider piping the output of samtools view -s to our program.

pub fn mapq_filter<VALUE: Into<u8>>(&mut self, value: VALUE) -> &mut Self

Exclude reads whose MAPQ (Mapping quality of position) is below this value. Defaults to zero i.e. do not exclude any read.

pub fn exclude_mapq_unavail(&mut self, value: bool) -> &mut Self

Exclude sequences with MAPQ unavailable. In the BAM format, a value of 255 in this column means MAPQ is unavailable. These reads are allowed by default, set this flag to exclude.

pub fn region(&mut self, value: String) -> &mut Self

Only keep reads passing through this region. If a BAM index is available with a name same as the BAM file but with the .bai suffix, the operation of selecting such reads will be faster. If you are using standard input as your input e.g. you are piping in the output from samtools, then you cannot use an index as a BAM filename is not available.

pub fn region_bed3<VALUE: Into<Bed3<i32, u64>>>( &mut self, value: VALUE, ) -> &mut Self

Only keep read data from this region. This is an internal option not exposed to the user, we will set it based on the other options that the user sets.

pub fn full_region(&mut self, value: bool) -> &mut Self

Only keep reads if they pass through the specified region in full. Related to the input --region; has no effect if that is not set.

pub fn build(&self) -> Result<InputBam, Error>

Builds a new InputBam.

Errors

If a required field has not been initialized.

Trait Implementations

impl Clone for InputBamBuilder

fn clone(&self) -> InputBamBuilder

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Default for InputBamBuilder

fn default() -> Self

Returns the “default value” for a type.