Tags: danielduyvo/FASTX.jl
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[Diff since v2.1.2](BioJulia/FASTX.jl@v2.1.2...v2.1.3) **Closed issues:** - FASTX.Records need a single-line representation (BioJulia#54) - Multiline FASTQ records? (BioJulia#78) - Migrate to new Automa release (BioJulia#82) - ERROR: Error when parsing FASTX file. Saw unexpected byte 'C' on line 1 (BioJulia#107) **Merged pull requests:** - Add short-form show for records (BioJulia#106) (@jakobnissen) - Migrate to Automa v1 (BioJulia#108) (@jakobnissen)
[Diff since v2.1.0](BioJulia/FASTX.jl@v2.1.0...v2.1.2) **Closed issues:** - package does not precompile (BioJulia#101) - Issue with QualityEncoding for the Solexa format (BioJulia#104) **Merged pull requests:** - Fix doc examples for writer with do-syntax (BioJulia#100) (@jakobnissen) - Bump ScanByte (BioJulia#102) (@jakobnissen) - Fix: Allow non-PHRED quality scores e.g. Solexa (BioJulia#105) (@jakobnissen)
[Diff since v2.1.0](BioJulia/FASTX.jl@v2.1.0...v2.1.1) **Merged pull requests:** - Fix doc examples for writer with do-syntax (BioJulia#100) (@jakobnissen) - Bump ScanByte (BioJulia#102) (@jakobnissen)
[Diff since v2.0.1](BioJulia/FASTX.jl@v2.0.1...v2.1.0) **Merged pull requests:** - Migrate from SnoopPrecompile to PrecompileTools (BioJulia#98) (@timholy) - Implement copy! for records (BioJulia#99) (@jakobnissen)
[Diff since v2.0.0](BioJulia/FASTX.jl@v2.0.0...v2.0.1) **Closed issues:** - Make Documenter preview builds work. (BioJulia#81) - subset FASTX.FASTQ.Record (BioJulia#89) - Make BioSequences an optional dependency (BioJulia#90) - Reading with the iteration protocole in 2.0 (BioJulia#94) - read! doesn't work in v2.0.0? (BioJulia#95) **Merged pull requests:** - Try to get preview build to work (BioJulia#86) (@kescobo) - Add SnoopPrecompile (BioJulia#87) (@jakobnissen) - Improve type stability slightly (BioJulia#88) (@jakobnissen) - Improve precompilation (BioJulia#92) (@jakobnissen) - Make BioSequences a weak dependency (BioJulia#93) (@jakobnissen) - Fix Base.read!(::Reader, ::Record) and add tests (BioJulia#96) (@jakobnissen)
[Diff since v1.3.0](BioJulia/FASTX.jl@v1.3.0...v2.0.0) **Closed issues:** - so slowly of extract sequence by coord (BioJulia#29) - Refactor tests (BioJulia#37) - Have accesor functions return views? (BioJulia#56) - Deal better with missingness (BioJulia#63) - bump compatibility for BioSymbols v5 and BioSequences v3? (BioJulia#65) - Documenter clearer that writers/readers take ownership of underlying IO (BioJulia#70) - Erratum in documentation (BioJulia#71) - Include period (.) in valid letters (BioJulia#73) - No good way to flush writers? (BioJulia#77) - Use ReTest or similar niceness? (BioJulia#83) **Merged pull requests:** - Return header, identifier and desc as string views (BioJulia#62) (@jakobnissen) - Rewrite for v2 (BioJulia#68) (@jakobnissen) - Clarify that streams take ownership of IO (BioJulia#72) (@jakobnissen) - Fix missing character in docs example (BioJulia#74) (@jakobnissen) - Use ReTest (BioJulia#84) (@kescobo) - Rollup of a few changes (BioJulia#85) (@jakobnissen)
## FASTX v1.3.0 [Diff since v1.2.0](BioJulia/FASTX.jl@v1.2.0...v1.3.0) **Closed issues:** - Converting FASTQ to FASTA (BioJulia#50) - TagBot trigger issue (BioJulia#51) - Why export only a few names? (BioJulia#57) - More conservative autodetection of sequence type (BioJulia#59) **Merged pull requests:** - Allow trailing whitespace in sequences (BioJulia#52) (@jakobnissen) - Transcode between FASTQ & FASTA files (BioJulia#53) (@SabrinaJaye) - Export all user-facing functions (BioJulia#58) (@jakobnissen) - Disallow record construction from anything (BioJulia#60) (@jakobnissen) - Update authors (BioJulia#61) (@jakobnissen) - Update Julia requirement to 1.6 (BioJulia#64) (@jakobnissen) - Bump BioSequences/BioSymbols to v3/v5 (BioJulia#66) (@jakobnissen) - Update TagBot.yml (BioJulia#67) (@CiaranOMara)
[Diff since v1.1.2](BioJulia/FASTX.jl@v1.1.2...v1.1.3) **Closed issues:** - Different slicing methods for FASTX.FASTA.sequences produces inconsistent behavior (BioJulia#23) **Merged pull requests:** - Fix zero-length copy (BioJulia#24) (@jakobnissen)
[Diff since v1.1.1](BioJulia/FASTX.jl@v1.1.1...v1.1.2) **Closed issues:** - Unexpected behaviour when reading FASTA files with read!(reader, record) (BioJulia#13) - LoadError: UndefVarError: LongSequence not defined during precompilation step (BioJulia#19) **Merged pull requests:** - Add docs on reading gzipped files (BioJulia#17) (@kescobo) - Remove use of internal `encode_copy!` [DO NOT MERGE] (BioJulia#18) (@jakobnissen) - Inbounds FASTQ parser (BioJulia#20) (@jakobnissen) - Run on Julia LTS (BioJulia#21) (@benjward)
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