Functions — github.com/aseyboldt/fastq-rs

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Functions63 in github.com/aseyboldt/fastq-rs

⨍ Functions 63 ◇ Types & classes 17

↓ 8 callersMethodeach

(self, mut func: F)

↓ 8 callersMethodlen

↓ 7 callersMethodwrite

(&self, writer: &mut W)

src/records.rs:93

↓ 6 callersMethoditer

Return an iterator over all fastq records in this record set.

↓ 5 callersMethodadvance

↓ 5 callersFunctionparse_path

Create a parser and guess the compression. At the moment this supports gzip, lz4 and plain fastq files. If the path is None, read from stdin. # Exam

↓ 5 callersMethodseq

src/records.rs:83

↓ 4 callersMethodread_into

(&mut self, reader: &mut R)

src/buffer.rs:74

↓ 4 callersFunctiontrim_winline

src/records.rs:67

↓ 3 callersMethoddata

src/buffer.rs:103

↓ 3 callersMethodget

↓ 3 callersMethodlen

src/buffer.rs:18

↓ 3 callersMethodn_free

src/buffer.rs:22

↓ 3 callersMethodparallel_each

Apply a function to each record, but distribute the work on a number of threads. # Parameters - `n_threads`: The number of worker threads to start.

↓ 3 callersMethodref_iter

Get a RecordRefIter for this parser. Should only be used in custom iteration scenarios.

↓ 2 callersMethodclean

Move data to the start of the buffer, freeing space at the end.

src/buffer.rs:51

↓ 2 callersMethodconsume

(&mut self, count: usize)

src/buffer.rs:108

↓ 2 callersMethodhead

src/records.rs:77

↓ 2 callersFunctionks_getuntil

examples/c/kseq.h:136

↓ 2 callersMethodqual

src/records.rs:88

↓ 2 callersMethodread

(&mut self, buffer: &mut [u8])

src/thread_reader.rs:91

↓ 2 callersMethodrecord_sets

Return the fastq records in chunks.

↓ 2 callersMethodreplace_buffer

(&mut self, mut buffer: Box<[u8]>)

src/buffer.rs:30

↓ 2 callersMethodto_owned_record

Copy the borrowed data array and return an owned record.

src/records.rs:167

↓ 2 callersMethodto_ref_record

(&self, buffer: &'a [u8])

src/records.rs:179

↓ 1 callersFunctionbuffer_channel

(bufsize: usize, queuelen: usize)

src/thread_reader.rs:13

↓ 1 callersFunctioneach_zipped

Step through two fastq files and call a callback for pairs of Records. The callback returns a tuple of bools that indicate for each parser if it shou

↓ 1 callersMethodfinished

src/thread_reader.rs:100

↓ 1 callersMethodnext_reader

src/thread_reader.rs:59

↓ 1 callersMethodpos

src/buffer.rs:26

↓ 1 callersFunctionread_header

(buffer: &[u8])

src/records.rs:138

↓ 1 callersFunctionread_sep

(buffer: &[u8])

src/records.rs:152

↓ 1 callersMethodserve

(&mut self, mut func: F)

src/thread_reader.rs:40

↓ 1 callersFunctionthread_reader

Wrap a reader in a background thread. This is only useful for readers that do expensive operations (eg decompression). The thread precomputes `queue

src/thread_reader.rs:182

Functionbufflen

Functioncorrect

src/thread_reader.rs:81

Functionempty_id

Methodfrom_buffer

(buffer: &[u8])

src/records.rs:202

Methodfrom_records

(buffer: Box<[u8]>, records: Vec<IdxRecord>)

Functionhuge_incomplete

Functionlength_mismatch

examples/multiple-files.rs:6

examples/alignment_count.rs:12

examples/fastq-count-thread.rs:6

examples/fastq-count.rs:6

examples/bio-count.rs:8

examples/c/readfq.cpp:8

examples/c/parse.c:9

Functionmissing_lines

src/buffer.rs:10

Create a new fastq parser.

(mut reader: R, buffsize: usize, queuelen: usize)

src/thread_reader.rs:126

Functionrefset_huge_incomplete

Functionrefset_incomplete

Functionsecond_idline

Functiontruncated

Methodvalidate_dna

Return true if the sequence contains only A, C, T and G. FIXME This might be much faster with a [bool; 256] array or using some simd instructions (eg

src/records.rs:19

Methodvalidate_dnan

Return true if the sequence contains only A, C, T, G and N. FIXME This might be much faster with a [bool; 256] array or using some simd instructions

src/records.rs:29

Functionwindows_lineend