Skip to content

Commit 30800e9

Browse files
GuilucandGuilucand
committed
Update README with new cli options
1 parent de89db6 commit 30800e9

File tree

2 files changed

+47
-35
lines changed

2 files changed

+47
-35
lines changed

‎README.md‎

Lines changed: 45 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -67,50 +67,62 @@ Here are all listed the available options for graph building:
6767
```
6868
> ggcat build --help
6969
USAGE:
70-
ggcat build [FLAGS] [OPTIONS] [--] [input]...
70+
ggcat build [FLAGS] [OPTIONS] --kmer-length <kmer-length> [--] [input]...
7171
7272
FLAGS:
73-
-c, --colors Enable colors
74-
--eulertigs Generate eulertigs instead of maximal unitigs
75-
-f, --forward-only Treats reverse complementary kmers as different
76-
-e, --generate-maximal-unitigs-links Generate maximal unitigs connections references, in BCALM2 format
77-
L:<+/->:<other id>:<+/->
78-
-h, --gfa Output the graph in GFA format
79-
-g, --greedy-matchtigs Generate greedy matchtigs instead of maximal unitigs
80-
-h, --help Prints help information
81-
--keep-temp-files Keep intermediate temporary files for debugging purposes
82-
--pathtigs Generate pathtigs instead of maximal unitigs
83-
-p, --prefer-memory Use all the given memory before writing to disk
84-
-V, --version Prints version information
73+
-c, --colors Enable colors
74+
--eulertigs Generate eulertigs instead of maximal unitigs
75+
--fast-eulertigs Generate eulertigs instead of maximal unitigs, faster version
76+
--fast-simplitigs Generate simplitigs instead of maximal unitigs, faster version
77+
-f, --forward-only Treats reverse complementary kmers as different
78+
-e, --generate-maximal-unitigs-links Generate maximal unitigs connections references, in BCALM2 format
79+
L:<+/->:<other id>:<+/->
80+
--gfa-v1 Output the graph in GFA format v1
81+
--gfa-v2 Output the graph in GFA format v2
82+
-g, --greedy-matchtigs Generate greedy matchtigs instead of maximal unitigs
83+
-h, --help Prints help information
84+
--keep-temp-files Keep intermediate temporary files for debugging purposes
85+
--pathtigs Generate pathtigs instead of maximal unitigs
86+
-p, --prefer-memory Use all the given memory before writing to disk
87+
-V, --version Prints version information
8588
8689
OPTIONS:
87-
-b, --buckets-count-log <buckets-count-log> The log2 of the number of buckets
88-
-d, --colored-input-lists <colored-input-lists>...
89-
-w, --hash-type <hash-type>
90-
Hash type used to identify kmers [default: Auto]
90+
-b, --buckets-count-log <buckets-count-log> The log2 of the number of buckets
91+
-d, --colored-input-lists <colored-input-lists>...
92+
The lists of input files with colors in format <COLOR_NAME><TAB><FILE_PATH>
9193
92-
-l, --input-lists <input-lists>... The lists of input files
93-
--intermediate-compression-level <intermediate-compression-level>
94-
The level of lz4 compression to be used for the intermediate files
94+
--disk-optimization-level <disk-optimization-level>
95+
Sets the level of disk optimization (0 disabled) [default: 5]
9596
96-
-k <klen> Specifies the k-mers length [default: 32]
97-
--last-step <last-step> [default: BuildUnitigs]
98-
-m, --memory <memory> Maximum memory usage (GB) [default: 2]
99-
-s, --min-multiplicity <min-multiplicity>
100-
Minimum multiplicity required to keep a kmer [default: 2]
97+
-w, --hash-type <hash-type>
98+
Hash type used to identify kmers [default: Auto]
99+
100+
-l, --input-lists <input-lists>... The lists of input files
101+
--intermediate-compression-level <intermediate-compression-level>
102+
The level of lz4 compression to be used for the intermediate files
103+
104+
-k, --kmer-length <kmer-length> Specifies the k-mers length
105+
--last-step <last-step> [default: BuildUnitigs]
106+
-m, --memory <memory>
107+
Maximum suggested memory usage (GB) The tool will try use only up to this GB of memory to store temporary
108+
files without writing to disk. This usage does not include the needed memory for the processing steps. GGCAT
109+
can allocate extra memory for files if the current memory is not enough to complete the current operation
110+
[default: 2]
111+
-s, --min-multiplicity <min-multiplicity>
112+
Minimum multiplicity required to keep a kmer [default: 2]
101113
102-
--mlen <mlen>
103-
Overrides the default m-mers (minimizers) length
114+
--minimizer-length <minimizer-length>
115+
Overrides the default m-mers (minimizers) length
104116
105-
-o, --output-file <output-file> [default: output.fasta.lz4]
106-
--step <step> [default: MinimizerBucketing]
107-
-t, --temp-dir <temp-dir>
108-
Directory for temporary files (default .temp_files) [default: .temp_files]
117+
-o, --output-file <output-file> [default: output.fasta.lz4]
118+
--step <step> [default: MinimizerBucketing]
119+
-t, --temp-dir <temp-dir>
120+
Directory for temporary files (default .temp_files) [default: .temp_files]
109121
110-
-j, --threads-count <threads-count> [default: 16]
122+
-j, --threads-count <threads-count> [default: 16]
111123
112124
ARGS:
113-
<input>... The input files
125+
<input>... The input files
114126
```
115127

116128
### Querying a graph

‎crates/cmdline/src/main.rs‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -179,11 +179,11 @@ struct AssemblerArgs {
179179
#[structopt(short = "g", long = "greedy-matchtigs", group = "output-mode")]
180180
pub greedy_matchtigs: bool,
181181

182-
/// Generate eulertigs instead of maximal unitigs
182+
/// Generate simplitigs instead of maximal unitigs, faster version
183183
#[structopt(long = "fast-simplitigs", group = "output-mode")]
184184
pub fast_simplitigs: bool,
185185

186-
/// Generate eulertigs instead of maximal unitigs
186+
/// Generate eulertigs instead of maximal unitigs, faster version
187187
#[structopt(long = "fast-eulertigs", group = "output-mode")]
188188
pub fast_eulertigs: bool,
189189

0 commit comments

Comments
 (0)