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github.com/BioJulia/FASTX.jl

Parse and process FASTA and FASTQ formatted files of biological sequences.
https://github.com/BioJulia/FASTX.jl

Internals: Use QualityScores iterator

jakobnissen opened this pull request 2 months ago
Delete workaround for compat with extensions

jakobnissen opened this pull request 2 months ago
Mark const fields as const

jakobnissen opened this pull request 2 months ago
Drop support for Julia <1.10

jakobnissen opened this pull request 2 months ago
Update TranscodingStreams compat to 0.11

jakobnissen opened this pull request 5 months ago
Upgrade CI

jakobnissen opened this pull request 6 months ago
Disable CI for x86 macOS-latest

jakobnissen opened this pull request 6 months ago
Import missing symbol in FASTQ

jakobnissen opened this pull request 6 months ago
Flip sticker

jakobnissen opened this pull request 6 months ago
Do not reach into TranscodingSteams internals

jakobnissen opened this pull request 9 months ago
Next release of TranscodingStreams will likely break this package

nhz2 opened this issue 9 months ago
Update issue and PR template to match BioJulia guidelines

jakobnissen opened this pull request about 1 year ago
Bump TranscodingStreams to 0.10

jakobnissen opened this pull request about 1 year ago
CompatHelper: bump compat for "TranscodingStreams" to "0.10"

github-actions[bot] opened this pull request about 1 year ago
Add Base.print(::IO, ::Index)

jakobnissen opened this pull request about 1 year ago
Make documentation more approachable

jakobnissen opened this pull request over 1 year ago
Drop ReTest test dep

jakobnissen opened this pull request over 1 year ago
Use new BioGenerics macros

jakobnissen opened this pull request over 1 year ago
Non-indexed FASTA: access sequence by genomic region

apraga opened this issue over 1 year ago
CompatHelper: bump compat for "Automa" to "1.0"

github-actions[bot] opened this pull request over 1 year ago
Migrate to Automa v1

jakobnissen opened this pull request over 1 year ago
ERROR: Error when parsing FASTX file. Saw unexpected byte 'C' on line 1

ljournot opened this issue over 1 year ago
Add short-form show for records

jakobnissen opened this pull request over 1 year ago
Fix: Allow non-PHRED quality scores e.g. Solexa

jakobnissen opened this pull request over 1 year ago
Issue with QualityEncoding for the Solexa format

anton083 opened this issue over 1 year ago
CompatHelper: bump compat for "ScanByte" to "0.4"

github-actions[bot] opened this pull request over 1 year ago
Bump ScanByte

jakobnissen opened this pull request over 1 year ago
package does not precompile

pfarndt opened this issue over 1 year ago
Fix doc examples for writer with do-syntax

jakobnissen opened this pull request over 1 year ago
Implement copy! for records

jakobnissen opened this pull request over 1 year ago
Migrate from SnoopPrecompile to PrecompileTools

timholy opened this pull request over 1 year ago
Fix Base.read!(::Reader, ::Record) and add tests

jakobnissen opened this pull request almost 2 years ago
read! doesn't work in v2.0.0?

banhbio opened this issue almost 2 years ago
Document `read!(::Reader, ::Record)`

jonathanBieler opened this issue almost 2 years ago
Make BioSequences a weak dependency

jakobnissen opened this pull request almost 2 years ago
Improve precompilation

jakobnissen opened this pull request almost 2 years ago
Consider despecializing AbstractFormattedIOs

jakobnissen opened this issue almost 2 years ago
Make BioSequences an optional dependency

jakobnissen opened this issue about 2 years ago
subset FASTX.FASTQ.Record

Liripo opened this issue about 2 years ago
Improve type stability slightly

jakobnissen opened this pull request over 2 years ago
Add SnoopPrecompile

jakobnissen opened this pull request over 2 years ago
Try to get preview build to work

kescobo opened this pull request over 2 years ago
Rollup of a few changes

jakobnissen opened this pull request over 2 years ago
Use ReTest

kescobo opened this pull request over 2 years ago
Use ReTest or similar niceness?

jakobnissen opened this issue over 2 years ago
Migrate to new Automa release

jakobnissen opened this issue over 2 years ago
Make Documenter preview builds work.

kescobo opened this issue over 2 years ago
Make constructing records less horribly inefficient

jakobnissen opened this issue over 2 years ago
Consider making `.data` fields of records const

jakobnissen opened this issue over 2 years ago
Multiline FASTQ records?

jakobnissen opened this issue over 2 years ago
No good way to flush writers?

jakobnissen opened this issue over 2 years ago
High level file processing

SabrinaJaye opened this issue over 2 years ago
[RFC]: Broaden characters allowed in FASTA sequences

jakobnissen opened this pull request almost 3 years ago
Fix missing character in docs example

jakobnissen opened this pull request almost 3 years ago
Include period (.) in valid letters

suyang-nju opened this issue almost 3 years ago
Clarify that streams take ownership of IO

jakobnissen opened this pull request almost 3 years ago
Erratum in documentation

reganbaucke opened this issue almost 3 years ago
Documenter clearer that writers/readers take ownership of underlying IO

spragud2 opened this issue almost 3 years ago
Change fileld field of records to Int

jakobnissen opened this pull request almost 3 years ago
Rewrite for v2

jakobnissen opened this pull request almost 3 years ago
Update TagBot.yml

CiaranOMara opened this pull request almost 3 years ago
Bump BioSequences/BioSymbols to v3/v5

jakobnissen opened this pull request almost 3 years ago
bump compatibility for BioSymbols v5 and BioSequences v3?

cecileane opened this issue almost 3 years ago
Update Julia requirement to 1.6

jakobnissen opened this pull request almost 3 years ago
Deal better with missingness

jakobnissen opened this issue almost 3 years ago
Return header, identifier and desc as string views

jakobnissen opened this pull request almost 3 years ago
Update authors

jakobnissen opened this pull request almost 3 years ago
Disallow record construction from anything

jakobnissen opened this pull request about 3 years ago
More conservative autodetection of sequence type

jakobnissen opened this issue about 3 years ago
Export all user-facing functions

jakobnissen opened this pull request about 3 years ago
Why export only a few names?

jakobnissen opened this issue about 3 years ago
Have accesor functions return views?

jakobnissen opened this issue about 3 years ago
Allow parsing FASTA record with no sequence

jakobnissen opened this pull request about 3 years ago
FASTX.Records need a single-line representation

jakobnissen opened this issue over 3 years ago
Transcode between FASTQ & FASTA files

SabrinaJaye opened this pull request over 3 years ago
Allow trailing whitespace in sequences

jakobnissen opened this pull request over 3 years ago
TagBot trigger issue

JuliaTagBot opened this issue over 3 years ago
Converting FASTQ to FASTA

jtackm opened this issue over 3 years ago
Allow trailing newlines for FASTQ files

jakobnissen opened this pull request over 3 years ago
malformed FASTQ file

jtackm opened this issue over 3 years ago
Call fill_ambiguous for FASTQ in all cases

motorny opened this pull request over 3 years ago
Disallow record construction from anything

jakobnissen opened this pull request over 3 years ago
Fix header code

jakobnissen opened this pull request over 3 years ago
FASTQ example added

BioTurboNick opened this pull request over 3 years ago
Model good behavior with do block syntax

BioTurboNick opened this pull request over 3 years ago
Use SIMD code generator

jakobnissen opened this pull request almost 4 years ago
Add quality and sequence iterator

jakobnissen opened this pull request almost 4 years ago
Performance comparison with Rust

jonathanBieler opened this issue almost 4 years ago
Fix FASTQ line counting bug

jakobnissen opened this pull request about 4 years ago
Fix description newline bug

jakobnissen opened this pull request about 4 years ago
Refactor tests

jakobnissen opened this issue about 4 years ago
Avoid copying data when extracting sequence

jakobnissen opened this pull request about 4 years ago
Subset fastq record using string syntax

tp2750 opened this pull request about 4 years ago
Subsetting a FASTQ record

tp2750 opened this issue about 4 years ago
Add header function

jakobnissen opened this pull request about 4 years ago
Is our FASTA format idiosyncratic?

jakobnissen opened this issue about 4 years ago
Add constant time fasta index seeking [NEED REVIEW]

jakobnissen opened this pull request over 4 years ago
Simplify seekrecord

jakobnissen opened this pull request over 4 years ago
so slowly of extract sequence by coord

panxiaoguang opened this issue over 4 years ago
Fix windows newline bug (issue 25)

jakobnissen opened this pull request over 4 years ago