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Doco fixes #54

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merged 5 commits into from
Aug 24, 2023
Merged

Doco fixes #54

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5e7f01d
summarise: Improve and sync full-help.
wwood Aug 24, 2023
03fb294
cli: Format descriptions betterer.
wwood Aug 24, 2023
635e46d
cli: Resolve conflicting short options.
wwood Aug 24, 2023
c6c9e45
cli: Further small improvements.
wwood Aug 24, 2023
1cdfaf7
src: Apply automated fixes for warnings.
wwood Aug 24, 2023
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4 changes: 2 additions & 2 deletions src/annotator/variant_annotation.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,7 @@ impl VariantAnnotations {
// debug!("Depth");
match annotation_type {
AnnotationType::Format => {
let mut genotype = genotype.unwrap();
let genotype = genotype.unwrap();
if !genotype.has_ad() {
// if there is no AD value calculate it now using likelihoods
Self::DepthPerAlleleBySample.annotate(
Expand Down Expand Up @@ -235,7 +235,7 @@ impl VariantAnnotations {
return AttributeObject::VecU8(statistics);
}
Self::DepthPerAlleleBySample => {
let mut genotype = genotype.unwrap();
let genotype = genotype.unwrap();
let alleles = vc.alleles.clone().into_iter().collect::<LinkedHashSet<_>>();
// debug!("Depth per allele alleles {:?}", &alleles);
// alleles.iter().for_each(|a| {
Expand Down
2 changes: 1 addition & 1 deletion src/assembly/kmer_counter.rs
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Expand Up @@ -80,7 +80,7 @@ impl KmerCounter {
kmer.len(),
self.kmer_length
);
let mut counts_from_map = self
let counts_from_map = self
.counts_by_kmer
.entry(kmer.clone())
.or_insert_with(|| CountedKmer::new(kmer));
Expand Down
109 changes: 46 additions & 63 deletions src/cli.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -190,22 +190,22 @@ fn add_thresholding_options(manual: Manual) -> Manual {
.help("Include secondary alignments. [default: not set] \n"),
)
.option(Opt::new("INT").long("--contig-end-exclusion").help(
"Exclude bases at the ends of reference \n
"Exclude bases at the ends of reference \
sequences from calculation [default: 0]",
))
.option(Opt::new("FLOAT").long("--trim-min").help(
"Remove this smallest fraction of positions \n
"Remove this smallest fraction of positions \
when calculating trimmed_mean [default: 0.00]",
))
.option(Opt::new("FLOAT").long("--trim-max").help(
"Maximum fraction for trimmed_mean \n
"Maximum fraction for trimmed_mean \
calculations [default: 1.00]",
))
.flag(Flag::new().long("--split-bams").help(
"Split the mapped read files up per reference.
Useful if you think run time is being hampered
by I/O. Most of the time this will not improve
performance and instead just increase disk usage. \n",
performance and instead just increase disk usage.",
)),
)
}
Expand Down Expand Up @@ -316,7 +316,7 @@ fn threads_options() -> Section {
.short("-t")
.help("Maximum number of threads used. [default: 10] \n"),
)
.option(Opt::new("INT").long("--parallel-genomes").short("-p").help(
.option(Opt::new("INT").long("--parallel-genomes").short("-P").help(
"Number of genomes to run in parallel. \
Increases memory usage linearly. \
Thread usage qill not exceed the value \
Expand Down Expand Up @@ -614,9 +614,9 @@ fn variant_calling_options_advanced() -> Section {
[default: 1] \n",
))
.flag(Flag::new().long("--use-adaptive-pruning").help(
"Use more advanced pruning algorithm to prune paths in
graph. Better suited when performing variant calling
on when depth along a genome is variable e.g. RNA
"Use more advanced pruning algorithm to prune paths in \
graph. Better suited when performing variant calling \
on when depth along a genome is variable e.g. RNA \
and exome data. \n",
))
.option(Opt::new("INT").long("--num-pruning-samples").help(
Expand Down Expand Up @@ -709,18 +709,16 @@ pub fn genotype_full_help() -> Manual {
)
.author(Author::new(crate::AUTHOR).email("rhys.newell94 near gmail.com"))
.description(
"
======= EXPERIMENTAL =======\n
lorikeet genotype discovers variants within a given set of reads and genomes and \n
clusters the variants into candidate strain haplotypes. Lorikeet uses UMAP and HDBSCAN \n
to cluster variants and an Expectation-Maximization algorithm to determine strain \n
haplotype abudnances within each samples. Additionally, calculate strain \n
diversity metrics like conANI, popANI, subpopANI, dN/dS, and the highly robust Hudson's Fst\n
\n
This process can be undertaken in several ways, for instance by specifying BAM files \n
or raw reads as input, using different mapping programs, thresholding read alignments \n
============================\
"
"\n\
EXPERIMENTAL!\n\n\
lorikeet genotype discovers variants within a given set of reads and genomes and \
clusters the variants into candidate strain haplotypes. Lorikeet uses UMAP and HDBSCAN \
to cluster variants and an Expectation-Maximization algorithm to determine strain \
haplotype abudnances within each samples. Additionally, calculate strain \
diversity metrics like conANI, popANI, subpopANI, dN/dS, and the highly robust Hudson's Fst\
\n\n\
This process can be undertaken in several ways, for instance by specifying BAM files \
or raw reads as input, using different mapping programs, thresholding read alignments."
);

manual = manual.custom(threads_options());
Expand All @@ -738,7 +736,7 @@ pub fn genotype_full_help() -> Manual {
.short("-o")
.long("--output-directory")
.help(
"Output directory. Folder will contain subfolders for each input genome \n
"Output directory. Folder will contain subfolders for each input genome \
[default: ./]",
),
)
Expand Down Expand Up @@ -797,16 +795,12 @@ pub fn call_full_help() -> Manual {
)
.author(Author::new(crate::AUTHOR).email("rhys.newell94 near gmail.com"))
.description(
"
===========================\n
lorikeet call discovers variants within a given set of reads and genomes using a local \n
reassembly algorithm based on the GATK HaplotypeCaller. Additionally, calculate strain \n
diversity metrics like conANI, popANI, subpopANI, dN/dS, and the highly robust Hudson's Fst \n\
\n
This process can be undertaken in several ways, for instance by specifying BAM files \n
or raw reads as input, using different mapping programs, thresholding read alignments \n
============================\n
"
"lorikeet call discovers variants within a given set of reads and genomes using a local \
reassembly algorithm based on the GATK HaplotypeCaller. Additionally, calculate strain \
diversity metrics like conANI, popANI, subpopANI, dN/dS, and the highly robust Hudson's Fst \
\n\n\
This process can be undertaken in several ways, for instance by specifying BAM files \
or raw reads as input, using different mapping programs, thresholding read alignments."
);

manual = manual.custom(threads_options());
Expand Down Expand Up @@ -883,19 +877,15 @@ pub fn consensus_full_help() -> Manual {
)
.author(Author::new(crate::AUTHOR).email("rhys.newell94 near gmail.com"))
.description(
"
===========================\n
lorikeet consensus discovers variants within a given set of reads and genomes using a local \n
reassembly algorithm based on the GATK HaplotypeCaller. Additionally, calculate strain \n
diversity metrics like conANI, popANI, subpopANI, dN/dS, and the highly robust Hudson's Fst \n\
"lorikeet consensus discovers variants within a given set of reads and genomes using a local \
reassembly algorithm based on the GATK HaplotypeCaller. Additionally, calculate strain \
diversity metrics like conANI, popANI, subpopANI, dN/dS, and the highly robust Hudson's Fst \
\n\
Lorikeet consensus also generates the consensus strain haplotypes for each sample and prints \
them as a FASTA file for each input genome in the output directory. \n\
them as a FASTA file for each input genome in the output directory. \
\n\
This process can be undertaken in several ways, for instance by specifying BAM files \n
or raw reads as input, using different mapping programs, thresholding read alignments \n
============================\
"
This process can be undertaken in several ways, for instance by specifying BAM files \
or raw reads as input, using different mapping programs, thresholding read alignments."
);

manual = manual.custom(threads_options());
Expand Down Expand Up @@ -972,19 +962,15 @@ pub fn summarise_full_help() -> Manual {
)
.author(Author::new(crate::AUTHOR).email("rhys.newell94 near gmail.com"))
.description(
"
===========================\n
lorikeet summarise uses a set of VCF files as input and calculates conANI, popANI,
subpopANI, and Fst metrics for the variants in each file. \n
\n
ANI metrics require coverage information to determine the number of shared bases
in each sample. VCF files do not provide this information, so the shared base size is just
the total size of the genome. In our experience, this doesn't really matter that much as
the ANI metrics are quite insensitive when provided low coverage samples anyway.
Fst tends to perform better for low and high coverage samples and does not require whole
genome coverage information.
============================\n
"
"lorikeet summarise uses a set of VCF files as input and calculates conANI, popANI, \
subpopANI, and Fst metrics for the variants in each file. \
\n\
ANI metrics require coverage information to determine the number of shared bases \
in each sample. VCF files do not provide this information, so the shared base size is just \
the total size of the genome. In our experience, this doesn't really matter that much as \
the ANI metrics are quite insensitive when provided low coverage samples anyway. \
Fst tends to perform better for low and high coverage samples and does not require whole \
genome coverage information."
);

manual = manual
Expand All @@ -1000,8 +986,8 @@ pub fn summarise_full_help() -> Manual {
.long("--vcfs")
.help("Paths to input VCF files. Can provide one or more. \n"),
)
.option(Opt::new("DIRECTORY").short("-o").long("--output").help(
"Output directory. Folder will contain subfolders for each input VCF \n
.option(Opt::new("DIRECTORY").short("-o").long("--output-directory").help(
"Output directory. Folder will contain subfolders for each input VCF \
[default: ./] \n",
))
.option(
Expand Down Expand Up @@ -1387,7 +1373,6 @@ Rhys J. P. Newell <rhys.newell near hdr.qut.edu.au>
.arg(
Arg::new("features-vcf")
.long("features-vcf")
.short('f')
.required(false),
)
.arg(
Expand All @@ -1398,7 +1383,7 @@ Rhys J. P. Newell <rhys.newell near hdr.qut.edu.au>
)
.arg(
Arg::new("parallel-genomes")
.short('p').long("parallel-genomes")
.short('P').long("parallel-genomes")
.value_parser(clap::value_parser!(usize))
.default_value("1"),
)
Expand Down Expand Up @@ -2172,7 +2157,6 @@ Rhys J. P. Newell <rhys.newell near hdr.qut.edu.au>
.arg(
Arg::new("features-vcf")
.long("features-vcf")
.short('f')
.required(false),
)
.arg(
Expand All @@ -2183,7 +2167,7 @@ Rhys J. P. Newell <rhys.newell near hdr.qut.edu.au>
)
.arg(
Arg::new("parallel-genomes")
.short('p').long("parallel-genomes")
.short('P').long("parallel-genomes")
.value_parser(clap::value_parser!(usize))
.default_value("1"),
)
Expand Down Expand Up @@ -2952,7 +2936,6 @@ Rhys J. P. Newell <rhys.newell near hdr.qut.edu.au>
.arg(
Arg::new("features-vcf")
.long("features-vcf")
.short('f')
.required(false),
)
.arg(
Expand All @@ -2963,7 +2946,7 @@ Rhys J. P. Newell <rhys.newell near hdr.qut.edu.au>
)
.arg(
Arg::new("parallel-genomes")
.short('p').long("parallel-genomes")
.short('P').long("parallel-genomes")
.value_parser(clap::value_parser!(usize))
.default_value("1"),
)
Expand Down Expand Up @@ -3563,7 +3546,7 @@ Rhys J. P. Newell <rhys.newell near hdr.qut.edu.au>
)
.arg(
Arg::new("output")
.long("output")
.long("output-directory")
.short('o')
.default_value("./"),
)
Expand Down