diff --git a/docs/Project.toml b/docs/Project.toml new file mode 100644 index 0000000..08045d2 --- /dev/null +++ b/docs/Project.toml @@ -0,0 +1,7 @@ +[deps] +BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59" +Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" + +[compat] +BioSequences = "3" +Documenter = "0.27" diff --git a/docs/src/fai.md b/docs/src/fai.md index 398dafd..186844d 100644 --- a/docs/src/fai.md +++ b/docs/src/fai.md @@ -131,4 +131,12 @@ julia> extract(reader, "seq1", 3:5) DocTestSetup = nothing ``` -FASTX.jl does not yet support indexing FASTQ files. \ No newline at end of file +FASTX.jl does not yet support indexing FASTQ files. + +### Reference: +```@docs +faidx +seekrecord +extract +Index +``` \ No newline at end of file diff --git a/docs/src/fasta.md b/docs/src/fasta.md index e9f412a..d29665c 100644 --- a/docs/src/fasta.md +++ b/docs/src/fasta.md @@ -55,4 +55,5 @@ Else, it will wrap lines to the given maximal width. ```@docs FASTA.Reader FASTA.Writer +validate_fasta ``` diff --git a/docs/src/fastq.md b/docs/src/fastq.md index 1002df7..5dd1972 100644 --- a/docs/src/fastq.md +++ b/docs/src/fastq.md @@ -112,6 +112,8 @@ QualityEncoding ### Reference: ```@docs quality +quality_scores +quality_header! ``` ## `FASTQReader` and `FASTQWriter` @@ -124,4 +126,5 @@ If set to a `Bool` value, the `Writer` will override the `Records`, without chan ```@docs FASTQ.Reader FASTQ.Writer +validate_fastq ``` \ No newline at end of file diff --git a/docs/src/records.md b/docs/src/records.md index d8c9b3f..654542a 100644 --- a/docs/src/records.md +++ b/docs/src/records.md @@ -56,3 +56,8 @@ UGCCCA julia> sequence(String, record) "UGCCCA" ``` + +### Reference: +```@docs +FASTA.Record! +``` \ No newline at end of file diff --git a/src/fasta/index.jl b/src/fasta/index.jl index fd82967..c244c02 100644 --- a/src/fasta/index.jl +++ b/src/fasta/index.jl @@ -23,7 +23,7 @@ Note that the FAI specs are stricter than FASTX.jl's definition of FASTA, such that some valid FASTA records may not be indexable. See the specs at: http://www.htslib.org/doc/faidx.html -See also: [FASTA.Reader](@ref) +See also: [`FASTA.Reader`](@ref) # Examples ```jldoctest