Functions — github.com/ArcInstitute/xsra

hub / github.com/ArcInstitute/xsra / functions

Functions145 in github.com/ArcInstitute/xsra

⨍ Functions 145◇ Types & classes 30

↓ 8 callersFunctionidentify_url

(accession: &str, options: &AccessionOptions)

src/prefetch/mod.rs:145

↓ 8 callersFunctionparse_url_with_fallback

( accession: &str, response: &str, full_quality: bool, lite_only: bool, provider: Provider

src/prefetch/mod.rs:114

↓ 7 callersFunctioncreate_fifo_if_absent

(path: OutputFileType)

src/output.rs:70

↓ 7 callersFunctionprefetch

(input: &MultiInputOptions, output_dir: Option<&str>)

src/prefetch/mod.rs:341

↓ 6 callersFunctiondescribe_inner

(accession: &str, skip: usize, limit: usize)

src/describe/mod.rs:28

↓ 5 callersFunctionbuild_writers

( outdir: Option<&str>, prefix: &str, compression: Compression, format: OutputFormat, num_

src/output.rs:177

↓ 5 callersFunctionparse_url

( accession: &str, response: &str, full_quality: bool, provider: Provider, )

src/prefetch/mod.rs:93

↓ 4 callersFunctioncreate_test_accession_options

Helper functions for test setup

src/prefetch/mod.rs:480

↓ 4 callersFunctiondownload_url

Download a file from a URL asynchronously

src/prefetch/mod.rs:267

↓ 3 callersFunctionbuild_path_name

( outdir: OutputFileType, prefix: &str, compression: Compression, format: OutputFormat, se

src/output.rs:161

↓ 3 callersFunctiondump

( input: &InputOptions, num_threads: u64, output_opts: &DumpOutput, filter_opts: FilterOptions

src/dump/mod.rs:145

↓ 3 callersMethodflush

(&mut self)

src/dump/output.rs:328

↓ 3 callersFunctionidentify_urls

Rate-limited version that processes multiple accessions by calling identify_url

src/prefetch/mod.rs:204

↓ 3 callersMethodingest

(&self, data: &[u8])

src/dump/output.rs:153

↓ 3 callersMethodpprint

(&self, wtr: &mut W)

src/dump/stats.rs:98

↓ 3 callersFunctionsum_slice

(vec: &[u64])

src/dump/stats.rs:124

↓ 3 callersMethodwrite_all_buffers

(&mut self, buffers: &mut [Vec<u8>], counts: &mut [usize])

src/dump/output.rs:241

↓ 2 callersMethodbitsize

(&self)

src/cli/recode.rs:98

↓ 2 callersFunctioncompression_passthrough

( writer: W, compression: Compression, num_threads: usize, )

src/output.rs:134

↓ 2 callersFunctioncreate_mock_server

(path: &str, status: usize, content: &str)

src/prefetch/mod.rs:491

↓ 2 callersFunctiondefault_accession_options

Test helper function to create default accession options

tests/dump.rs:18

↓ 2 callersMethoddownload_small_variable_sra

Download a small SRA file with variable-length segments for fast VBINSEQ testing

tests/fixtures/setup.rs:85

↓ 2 callersFunctiondownload_url_gcp

Download a file from a GCP URL using gsutil

src/prefetch/mod.rs:294

↓ 2 callersFunctiondownload_url_test_setup

()

src/prefetch/mod.rs:503

↓ 2 callersMethodext

(&self)

src/output.rs:32

↓ 2 callersFunctionget_num_records

(path: &str)

src/utils.rs:4

↓ 2 callersMethodinc_filter_size

(&mut self, seg_id: usize)

src/dump/stats.rs:86

↓ 2 callersMethodinc_filter_type

(&mut self, seg_id: usize)

src/dump/stats.rs:92

↓ 2 callersMethodinc_reads

(&mut self, seg_id: usize)

src/dump/stats.rs:79

↓ 2 callersMethodinc_spots

(&mut self)

src/dump/stats.rs:76

↓ 2 callersMethodpaired

(&self)

src/cli/recode.rs:31

↓ 2 callersMethodsegment_lengths

(&self)

src/describe/stats.rs:100

↓ 2 callersMethodthreads

(&self)

src/cli/runtime.rs:13

↓ 2 callersFunctionwrite_fasta

( wtr: &mut W, segment: &Segment<'_>, accession_prefix: Option<&str>, include_sid: bool, )

src/dump/utils.rs:62

↓ 2 callersFunctionwrite_fastq

( wtr: &mut W, segment: &Segment<'_>, accession_prefix: Option<&str>, include_sid: bool, )

src/dump/utils.rs:40

↓ 2 callersFunctionwriter_from_path

(path: OutputFileType)

src/output.rs:116

↓ 1 callersMethodaccession_set

(&self)

src/cli/input.rs:29

↓ 1 callersMethodadd

(mut self, other: Self)

src/dump/stats.rs:30

↓ 1 callersFunctionbuild_segment_writer

( outdir: Option<&str>, prefix: &str, compression: Compression, format: OutputFormat, num_

src/dump/output.rs:48

↓ 1 callersFunctioncalculate_average_quality

(qual: &[u8])

src/describe/mod.rs:15

↓ 1 callersMethodcreate_corrupt_sra

Create a corrupt SRA file by truncating a valid one

tests/fixtures/setup.rs:163

↓ 1 callersMethodcreate_invalid_sra

Create an invalid SRA file (not actually SRA format)

tests/fixtures/setup.rs:186

↓ 1 callersFunctiondescribe

(input: &InputOptions, opts: &DescribeOptions)

src/describe/mod.rs:72

↓ 1 callersMethoddownload_small_fixed_sra

Download a small SRA file with fixed-length segments for fast BINSEQ testing

tests/fixtures/setup.rs:124

↓ 1 callersMethodextended_sid

(&self)

src/cli/recode.rs:39

↓ 1 callersMethodextension

(&self)

src/cli/recode.rs:118

↓ 1 callersMethodgenerate_local_buffers

Return local buffers to mimic the expected writer buffers on-thread

src/dump/output.rs:41

↓ 1 callersMethodinclude_sid

(&self)

src/cli/dump.rs:70

↓ 1 callersFunctioninitialize_logger

()

src/main.rs:21

↓ 1 callersFunctionis_rate_limited

Checks if the response from NCBI indicates rate limiting

src/prefetch/mod.rs:21

↓ 1 callersFunctionlaunch_threads

( path: &str, num_threads: u64, records_per_thread: u64, remainder: u64, writer: Arc<Mutex

src/dump/mod.rs:23

↓ 1 callersMethodname

(&self)

src/cli/recode.rs:90

↓ 1 callersFunctionpass_url_filter

Checks if a line in the response is a URL and passes all the filters

src/prefetch/mod.rs:83

↓ 1 callersMethodpprint

(&self, wtr: &mut W)

src/describe/stats.rs:104

↓ 1 callersMethodprimary_sid

(&self)

src/cli/recode.rs:35

↓ 1 callersFunctionquery_entrez

(accession: &str)

src/prefetch/mod.rs:38

↓ 1 callersFunctionrecode

(args: &RecodeArgs)

src/recode/mod.rs:22

↓ 1 callersFunctionrecode_inner

( accession: &str, output_path: &str, primary_sid: usize, extended_sid: Option<usize>, bit

↓ 1 callersMethodsetup_fixtures

Internal method that does the actual fixture setup work

tests/fixtures/setup.rs:50

↓ 1 callersMethodto_format

(self)

src/cli/recode.rs:125

↓ 1 callersMethodurl_prefix

(&self)

src/cli/input.rs:82

↓ 1 callersMethodvalidate

(&self)

src/cli/recode.rs:21

↓ 1 callersMethodwrite

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

src/dump/output.rs:323

↓ 1 callersFunctionwrite_segment_to_buffer_set

( buffers: &mut [Vec<u8>], segment: &Segment<'_>, format: OutputFormat, accession_prefix: Opti

src/dump/utils.rs:8

↓ 1 callersMethodwrite_to_handles

(&mut self)

src/dump/output.rs:223

Methodaverage

(vec: Vec<Vec<f64>>)

src/describe/stats.rs:88

Functionbuild_writers_creates_directory_and_writers_for_included_segments

()

src/output.rs:344

Functionbuild_writers_stdout_when_no_outdir

()

src/output.rs:407

Functionbuild_writers_uses_empty_writer_for_filtered_segments

()

src/output.rs:377

Functioncreate_fifo_if_absent_creates_new_fifo_non_unix

()

src/output.rs:329

Functioncreate_fifo_if_absent_creates_new_fifo_unix

()

src/output.rs:315

Functioncreate_fifo_if_absent_existing_fifo_file

()

src/output.rs:260

Functioncreate_fifo_if_absent_existing_file_non_unix

()

src/output.rs:298

Functioncreate_fifo_if_absent_existing_non_fifo_file

()

src/output.rs:281

Functioncreate_fifo_if_absent_fails_with_non_fifo_output

Functiondescribe_inner_handles_invalid_sra_file

()

src/describe/mod.rs:96

Functiondirect_writer_write_all_buffers_happy_path_with_empty_segment

()

src/dump/output.rs:335

Functiondownload_url_fails_with_404_error

()

src/prefetch/mod.rs:808

Functiondownload_url_succeeds_with_valid_content

()

src/prefetch/mod.rs:792

Methoddrop

(&mut self)

src/dump/output.rs:169

Methodensure_fixtures

Ensure all test fixtures exist, downloading or creating them if needed. This method is thread-safe and will only run the setup once, even if called fr

tests/fixtures/setup.rs:35

Methodext

(&self)

src/cli/dump.rs:87

Functionfallback_falls_back_when_lite_unavailable

()

src/prefetch/mod.rs:600

Functionfallback_handles_conflicting_flags

()

src/prefetch/mod.rs:627

Functionfallback_prefers_requested_quality_when_both_available

()

src/prefetch/mod.rs:576

Functionfallback_prevents_when_lite_only_true

()

src/prefetch/mod.rs:610

Functionfallback_returns_none_when_no_urls

()

src/prefetch/mod.rs:635

Functionfallback_works_with_lite_only_when_available

()

src/prefetch/mod.rs:617

Methodfmt

This trait requires `fmt` with this exact signature.

src/output.rs:51

Methodfmt

(&self, f: &mut std::fmt::Formatter<'_>)

src/cli/input.rs:73

Methodfmt

(&self, f: &mut std::fmt::Formatter<'_>)

src/describe/stats.rs:10

Methodfrom

(ty: SegmentType)

src/describe/stats.rs:27

Functionidentify_url_fails_with_unsupported_provider

()

src/prefetch/mod.rs:666

Functionidentify_url_fails_with_zero_retries

()

src/prefetch/mod.rs:681

Functionidentify_url_succeeds_with_proper_provider

()

src/prefetch/mod.rs:643

Functionidentify_urls_handles_mixed_success_failure

()

src/prefetch/mod.rs:747

Functionidentify_urls_succeeds_with_multiple_accessions

()

src/prefetch/mod.rs:695

Functionis_rate_limited_detects_rate_limit_errors

()

src/prefetch/mod.rs:517

next →1–100 of 145, ranked by callers