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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 3 months ago
Delete workaround for compat with extensions

jakobnissen opened this pull request 3 months ago
Mark const fields as const

jakobnissen opened this pull request 3 months ago
Drop support for Julia <1.10

jakobnissen opened this pull request 3 months ago
Update TranscodingStreams compat to 0.11

jakobnissen opened this pull request 7 months ago
Upgrade CI

jakobnissen opened this pull request 7 months ago
Disable CI for x86 macOS-latest

jakobnissen opened this pull request 7 months ago
Import missing symbol in FASTQ

jakobnissen opened this pull request 7 months ago
Flip sticker

jakobnissen opened this pull request 7 months ago
Do not reach into TranscodingSteams internals

jakobnissen opened this pull request 10 months ago
Next release of TranscodingStreams will likely break this package

nhz2 opened this issue 10 months ago
Update issue and PR template to match BioJulia guidelines

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

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

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

jakobnissen opened this pull request over 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 almost 2 years 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 about 2 years ago
Improve precompilation

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

jakobnissen opened this issue about 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 about 3 years ago
Deal better with missingness

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

jakobnissen opened this pull request about 3 years ago
Update authors

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

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

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

jakobnissen opened this pull request over 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 almost 4 years ago
Fix header code

jakobnissen opened this pull request almost 4 years ago
FASTQ example added

BioTurboNick opened this pull request almost 4 years ago
Model good behavior with do block syntax

BioTurboNick opened this pull request almost 4 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 over 4 years ago
Avoid copying data when extracting sequence

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

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

tp2750 opened this issue over 4 years ago
Add header function

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

jakobnissen opened this issue over 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