default to consensus mode

Author: amkram

docs/cli-reference.md

@@ -16,7 +16,7 @@ Use `--help` for common options or `--help-all` for the full list.
 | `-o, --output` | Output file prefix | derived from reads filename |
 | `-t, --threads` | Number of threads | `1` |
 | `-a, --aligner` | `minimap2` or `bwa` | `minimap2` |
-| `--stop` | Stop after: `index`, `place`, `align`, `genotype`, `consensus` | `place` |
+| `--stop` | Stop after: `index`, `place`, `align`, `genotype`, `consensus` | `consensus` |
 | `--meta` | Enable metagenomic mode | off |
 | `-v, --verbose` | Verbose output | off |
 | `-q, --quiet` | Errors only | off |

docs/index.md

@@ -10,8 +10,8 @@ panmap takes sequencing reads and a pangenome in [PanMAN](https://github.com/Tur
 # Install
 conda install -c bioconda panmap
 
-# Place and genotype paired-end reads
-panmap ref.panman reads_R1.fq reads_R2.fq --stop genotype -t 8 -o sample
+# Place, genotype, and build consensus
+panmap ref.panman reads_R1.fq reads_R2.fq -t 8 -o sample
 
 # Metagenomic abundance estimation
 panmap ref.panman reads.fq --meta --index ref.idx -t 8 -o sample

docs/quickstart.md

@@ -8,7 +8,7 @@ panmap <panman> [reads1.fq] [reads2.fq] [options]
 
 ## Pipeline
 
-panmap runs five stages in sequence. By default it stops after **placement**. Use `--stop` to run further.
+panmap runs five stages in sequence. By default it runs through **consensus**. Use `--stop` to stop earlier.
 
 ```
 index  -->  place  -->  align  -->  genotype  -->  consensus
@@ -20,8 +20,7 @@ index  -->  place  -->  align  -->  genotype  -->  consensus
 Place reads onto the pangenome, align to the closest reference, call variants, and generate a consensus:
 
 ```bash
-panmap ref.panman reads_R1.fq reads_R2.fq \
-  --stop consensus -t 8 -o sample
+panmap ref.panman reads_R1.fq reads_R2.fq -t 8 -o sample
 ```
 
 This produces `sample.bam`, `sample.vcf`, and `sample.consensus.fa`.

docs/single-sample.md

@@ -5,24 +5,24 @@ The default mode. Places reads from one sample onto the pangenome tree, aligns t
 ## Basic usage
 
 ```bash
-# Place reads (default -- stops after placement)
+# Run full pipeline (default -- through consensus)
 panmap ref.panman reads_R1.fq reads_R2.fq -t 8 -o sample
 
-# Run through genotyping
-panmap ref.panman reads_R1.fq reads_R2.fq --stop consensus -t 8 -o sample
+# Stop at an earlier stage
+panmap ref.panman reads_R1.fq reads_R2.fq --stop genotype -t 8 -o sample
 ```
 
 ## Pipeline stages
 
-By default, panmap stops after **placement**. Use `--stop` to control how far the pipeline runs.
+By default, panmap runs through **consensus**. Use `--stop` to stop at an earlier stage.
 
 | Stage | `--stop` value | Output | Description |
 |-------|---------------|--------|-------------|
 | Index | `index` | `<prefix>.idx` | Builds seed index from the PanMAN |
-| Place | `place` (default) | `<prefix>.placement.tsv` | Places reads onto the pangenome tree |
+| Place | `place` | `<prefix>.placement.tsv` | Places reads onto the pangenome tree |
 | Align | `align` | `<prefix>.bam` | Aligns reads to closest reference |
 | Genotype | `genotype` | `<prefix>.vcf` | Calls variants from alignments |
-| Consensus | `consensus` | `<prefix>.consensus.fa` | Generates consensus FASTA from variants |
+| Consensus | `consensus` (default) | `<prefix>.consensus.fa` | Generates consensus FASTA from variants |
 
 !!! note
     When `--stop genotype` is used, `--force-leaf` is enabled automatically.
@@ -74,7 +74,7 @@ panmap examples/data/sars_20000_twilight_dipper.panman \
 | `-o, --output` | Output file prefix | derived from reads filename |
 | `-t, --threads` | Number of threads | `1` |
 | `-a, --aligner` | `minimap2` or `bwa` | `minimap2` |
-| `--stop` | Stop after: `index`, `place`, `align`, `genotype` | `place` |
+| `--stop` | Stop after: `index`, `place`, `align`, `genotype`, `consensus` | `consensus` |
 | `--force-leaf` | Restrict placement to leaf nodes | off (auto-enabled with `--stop genotype`) |
 | `--refine` | Alignment-based refinement of top candidates | off |
 

src/main.cpp

@@ -1708,7 +1708,7 @@ int main(int argc, char** argv) {
         ("version,V", "Show version")
         ("output,o", po::value<std::string>(&cfg.output), "Output prefix")
         ("threads,t", po::value<int>(&cfg.threads)->default_value(1), "Threads")
-        ("stop", po::value<std::string>()->default_value("place"), "Stop after: index|place|align|genotype|consensus")
+        ("stop", po::value<std::string>()->default_value("consensus"), "Stop after: index|place|align|genotype|consensus")
         ("meta", po::bool_switch(&cfg.metagenomic), "Metagenomic mode (for more options, see --help-all)")
         ("aligner,a", po::value<std::string>(&cfg.aligner)->default_value("minimap2"), "Aligner: minimap2|bwa")
         ("verbose,v", po::bool_switch(&cfg.verbose), "Verbose output")