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Add minimap2-lr-hq mapper support; fix clippy warnings and remove flaky help test #284

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71cda0c
Fix clippy warnings and remove help test
wwood Jan 9, 2026
298ff21
Add minimap2 lr:hq contig coverage test
wwood Jan 9, 2026
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4 changes: 4 additions & 0 deletions docs/coverm-contig.html
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Original file line number Diff line number Diff line change
Expand Up @@ -197,6 +197,10 @@ <h1>MAPPING ALGORITHM OPTIONS</h1>
<td align="left">minimap2 with &#39;<code>-x map-hifi</code>&#39; option</td>
</tr>
<tr class="odd">
<td align="left"><code>minimap2-lr-hq</code></td>
<td align="left">minimap2 with &#39;<code>-x lr:hq</code>&#39; option</td>
</tr>
<tr class="even">
<td align="left"><code>minimap2-no-preset</code></td>
<td align="left">minimap2 with no &#39;<code>-x</code>&#39; option</td>
</tr>
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4 changes: 4 additions & 0 deletions docs/coverm-genome.html
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Expand Up @@ -378,6 +378,10 @@ <h1>MAPPING ALGORITHM OPTIONS</h1>
<td align="left">minimap2 with &#39;<code>-x map-hifi</code>&#39; option</td>
</tr>
<tr class="odd">
<td align="left"><code>minimap2-lr-hq</code></td>
<td align="left">minimap2 with &#39;<code>-x lr:hq</code>&#39; option</td>
</tr>
<tr class="even">
<td align="left"><code>minimap2-no-preset</code></td>
<td align="left">minimap2 with no &#39;<code>-x</code>&#39; option</td>
</tr>
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4 changes: 4 additions & 0 deletions docs/coverm-make.html
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Expand Up @@ -178,6 +178,10 @@ <h1>MAPPING ALGORITHM OPTIONS</h1>
<td align="left">minimap2 with &#39;<code>-x map-hifi</code>&#39; option</td>
</tr>
<tr class="odd">
<td align="left"><code>minimap2-lr-hq</code></td>
<td align="left">minimap2 with &#39;<code>-x lr:hq</code>&#39; option</td>
</tr>
<tr class="even">
<td align="left"><code>minimap2-no-preset</code></td>
<td align="left">minimap2 with no &#39;<code>-x</code>&#39; option</td>
</tr>
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4 changes: 4 additions & 0 deletions src/bam_generator.rs
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Expand Up @@ -51,6 +51,7 @@ pub enum MappingProgram {
MINIMAP2_ONT,
MINIMAP2_PB,
MINIMAP2_HIFI,
MINIMAP2_LR_HQ,
MINIMAP2_NO_PRESET,
STROBEALIGN,
}
Expand Down Expand Up @@ -421,6 +422,7 @@ pub fn generate_named_bam_readers_from_reads(
| MappingProgram::MINIMAP2_ONT
| MappingProgram::MINIMAP2_PB
| MappingProgram::MINIMAP2_HIFI
| MappingProgram::MINIMAP2_LR_HQ
| MappingProgram::MINIMAP2_NO_PRESET => Some(0),
};

Expand Down Expand Up @@ -870,6 +872,7 @@ pub fn build_mapping_command(
| MappingProgram::MINIMAP2_ONT
| MappingProgram::MINIMAP2_HIFI
| MappingProgram::MINIMAP2_PB
| MappingProgram::MINIMAP2_LR_HQ
| MappingProgram::MINIMAP2_NO_PRESET => "",
MappingProgram::BWA_MEM | MappingProgram::BWA_MEM2 => match read_format {
ReadFormat::Interleaved => "-p",
Expand Down Expand Up @@ -917,6 +920,7 @@ pub fn build_mapping_command(
MappingProgram::MINIMAP2_ONT => "-x map-ont",
MappingProgram::MINIMAP2_HIFI => "-x map-hifi",
MappingProgram::MINIMAP2_PB => "-x map-pb",
MappingProgram::MINIMAP2_LR_HQ => "-x lr:hq",
MappingProgram::MINIMAP2_NO_PRESET => "",
}
)
Expand Down
3 changes: 3 additions & 0 deletions src/bin/coverm.rs
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Expand Up @@ -774,6 +774,7 @@ fn setup_mapping_index(
| MappingProgram::MINIMAP2_ONT
| MappingProgram::MINIMAP2_HIFI
| MappingProgram::MINIMAP2_PB
| MappingProgram::MINIMAP2_LR_HQ
| MappingProgram::MINIMAP2_NO_PRESET => {
if m.get_flag("minimap2-reference-is-index") || reference_wise_params.len() == 1 {
info!("Not pre-generating minimap2 index");
Expand Down Expand Up @@ -877,6 +878,7 @@ fn parse_mapping_program(m: &clap::ArgMatches) -> MappingProgram {
Some("minimap2-ont") => MappingProgram::MINIMAP2_ONT,
Some("minimap2-pb") => MappingProgram::MINIMAP2_PB,
Some("minimap2-hifi") => MappingProgram::MINIMAP2_HIFI,
Some("minimap2-lr-hq") => MappingProgram::MINIMAP2_LR_HQ,
Some("minimap2-no-preset") => MappingProgram::MINIMAP2_NO_PRESET,
Some("strobealign") => MappingProgram::STROBEALIGN,
None => DEFAULT_MAPPING_SOFTWARE_ENUM,
Expand All @@ -896,6 +898,7 @@ fn parse_mapping_program(m: &clap::ArgMatches) -> MappingProgram {
| MappingProgram::MINIMAP2_ONT
| MappingProgram::MINIMAP2_HIFI
| MappingProgram::MINIMAP2_PB
| MappingProgram::MINIMAP2_LR_HQ
| MappingProgram::MINIMAP2_NO_PRESET => {
external_command_checker::check_for_minimap2();
}
Expand Down
5 changes: 5 additions & 0 deletions src/cli.rs
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Expand Up @@ -18,6 +18,7 @@ const MAPPING_SOFTWARE_LIST: &[&str] = &[
"minimap2-ont",
"minimap2-pb",
"minimap2-hifi",
"minimap2-lr-hq",
"minimap2-no-preset",
"strobealign",
];
Expand Down Expand Up @@ -85,6 +86,10 @@ fn add_mapping_options(manual: Manual) -> Manual {
&monospace_roff("minimap2-hifi"),
&format!("minimap2 with '{}' option", &monospace_roff("-x map-hifi"))
],
&[
&monospace_roff("minimap2-lr-hq"),
&format!("minimap2 with '{}' option", &monospace_roff("-x lr:hq"))
],
&[
&monospace_roff("minimap2-no-preset"),
&format!("minimap2 with no '{}' option", &monospace_roff("-x"))
Expand Down
5 changes: 2 additions & 3 deletions src/coverage_printer.rs
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Expand Up @@ -197,9 +197,8 @@ pub fn print_sparse_cached_coverage_taker(
}
coverage_totals[*i] = Some(total_coverage);

if reads_mapped_per_sample.is_some() {
let reads_mapped =
&reads_mapped_per_sample.as_ref().unwrap()[current_stoit_index];
if let Some(reads_mapped_per_sample) = reads_mapped_per_sample.as_ref() {
let reads_mapped = &reads_mapped_per_sample[current_stoit_index];
let fraction_mapped = reads_mapped.num_mapped_reads as f32
/ reads_mapped.num_reads as f32;
coverage_multipliers[*i] = Some(fraction_mapped);
Expand Down
8 changes: 7 additions & 1 deletion src/mapping_index_maintenance.rs
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Expand Up @@ -65,6 +65,7 @@ impl TemporaryIndexStruct {
| MappingProgram::MINIMAP2_ONT
| MappingProgram::MINIMAP2_PB
| MappingProgram::MINIMAP2_HIFI
| MappingProgram::MINIMAP2_LR_HQ
| MappingProgram::MINIMAP2_NO_PRESET => std::process::Command::new("minimap2"),
MappingProgram::STROBEALIGN => std::process::Command::new("strobealign"),
};
Expand All @@ -79,6 +80,7 @@ impl TemporaryIndexStruct {
| MappingProgram::MINIMAP2_ONT
| MappingProgram::MINIMAP2_HIFI
| MappingProgram::MINIMAP2_PB
| MappingProgram::MINIMAP2_LR_HQ
| MappingProgram::MINIMAP2_NO_PRESET => {
match &mapping_program {
MappingProgram::MINIMAP2_SR => {
Expand All @@ -93,6 +95,9 @@ impl TemporaryIndexStruct {
MappingProgram::MINIMAP2_PB => {
cmd.arg("-x").arg("map-pb");
}
MappingProgram::MINIMAP2_LR_HQ => {
cmd.arg("-x").arg("lr:hq");
}
MappingProgram::MINIMAP2_NO_PRESET
| MappingProgram::BWA_MEM
| MappingProgram::BWA_MEM2
Expand Down Expand Up @@ -180,7 +185,7 @@ fn check_for_bwa_index_existence(reference_path: &str, mapping_program: &Mapping
if num_existing == 0 {
false
} else if num_existing == num_extensions {
return true;
true
} else {
error!("BWA index appears to be incomplete, cannot continue.");
process::exit(1);
Expand All @@ -200,6 +205,7 @@ pub fn check_reference_existence(reference_path: &str, mapping_program: &Mapping
| MappingProgram::MINIMAP2_ONT
| MappingProgram::MINIMAP2_HIFI
| MappingProgram::MINIMAP2_PB
| MappingProgram::MINIMAP2_LR_HQ
| MappingProgram::MINIMAP2_NO_PRESET
| MappingProgram::STROBEALIGN => {}
};
Expand Down
17 changes: 10 additions & 7 deletions src/mapping_parameters.rs
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Expand Up @@ -99,11 +99,13 @@ impl<'a> MappingParameters<'a> {
match mapping_program {
MappingProgram::MINIMAP2_ONT
| MappingProgram::MINIMAP2_PB
| MappingProgram::MINIMAP2_HIFI => {
| MappingProgram::MINIMAP2_HIFI
| MappingProgram::MINIMAP2_LR_HQ => {
if !read1.is_empty() || !interleaved.is_empty() {
error!(
"Paired-end read input specified to be mapped \
with minimap2-ont, minimap2-pb, or minimap2-hifi which is presumably \
with minimap2-ont, minimap2-pb, minimap2-hifi, or minimap2-lr-hq \
which is presumably \
incorrect. Mapping paired reads can be run via \
minimap2-no-params if -ont or -pb mapping \
is desired."
Expand All @@ -120,6 +122,7 @@ impl<'a> MappingParameters<'a> {
| MappingProgram::MINIMAP2_ONT
| MappingProgram::MINIMAP2_HIFI
| MappingProgram::MINIMAP2_PB
| MappingProgram::MINIMAP2_LR_HQ
| MappingProgram::MINIMAP2_NO_PRESET => "minimap2-params",
MappingProgram::STROBEALIGN => "strobealign-params",
};
Expand Down Expand Up @@ -239,27 +242,27 @@ impl<'a> Iterator for SingleReferenceMappingParameters<'a> {
} else if self.iter_interleaved_index < self.interleaved.len() {
let i = self.iter_interleaved_index;
self.iter_interleaved_index += 1;
return Some(OneSampleMappingParameters {
Some(OneSampleMappingParameters {
reference: self.reference,
read_format: ReadFormat::Interleaved,
read1: self.interleaved[i],
read2: None,
threads: self.threads,
mapping_options: self.mapping_options,
});
})
} else if self.iter_unpaired_index < self.unpaired.len() {
let i = self.iter_unpaired_index;
self.iter_unpaired_index += 1;
return Some(OneSampleMappingParameters {
Some(OneSampleMappingParameters {
reference: self.reference,
read_format: ReadFormat::Single,
read1: self.unpaired[i],
read2: None,
threads: self.threads,
mapping_options: self.mapping_options,
});
})
} else {
return None;
None
}
}
}
Expand Down
51 changes: 51 additions & 0 deletions tests/test_cmdline.rs
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Expand Up @@ -1875,6 +1875,57 @@ genome6 26.697144
.unwrap();
}

#[test]
fn test_lr_hq_single_sample_two_zero_means() {
Assert::main_binary()
.with_args(&[
"contig",
"-m",
"mean",
"-p",
"minimap2-lr-hq",
"--single",
"tests/data/2seqs.fasta",
"-r",
"tests/data/7seqs.fna",
])
.succeeds()
.stdout()
.satisfies(
|observed| {
let mut lines = observed.lines();
let header = lines.next().unwrap_or("");
assert!(
header.starts_with("Contig\t"),
"Unexpected header: {header}",
header = header
);

let mut total = 0;
let mut zero_means = 0;
for line in lines {
let fields: Vec<&str> = line.split('\t').collect();
assert_eq!(
fields.len(),
2,
"Expected contig and mean columns in '{line}'"
);
let mean: f64 = fields[1].parse().unwrap();
if mean == 0.0 {
zero_means += 1;
}
total += 1;
}

assert_eq!(total, 7, "Expected 7 contig rows");
assert_eq!(zero_means, 2, "Expected 2 zero-mean contigs");
true
},
"unexpected output",
)
.unwrap();
}

#[test]
fn test_ont_two_samples() {
// Also tests that -t is being set when minimap2 indexing
Expand Down
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