diff --git a/docs/coverm-contig.html b/docs/coverm-contig.html
index 9fcac82..f3fca67 100644
--- a/docs/coverm-contig.html
+++ b/docs/coverm-contig.html
@@ -197,6 +197,10 @@ MAPPING ALGORITHM OPTIONS
minimap2 with '-x map-hifi' option |
+minimap2-lr-hq |
+minimap2 with '-x lr:hq' option |
+
+
minimap2-no-preset |
minimap2 with no '-x' option |
diff --git a/docs/coverm-genome.html b/docs/coverm-genome.html
index e8b7362..54bd6c1 100644
--- a/docs/coverm-genome.html
+++ b/docs/coverm-genome.html
@@ -378,6 +378,10 @@ MAPPING ALGORITHM OPTIONS
minimap2 with '-x map-hifi' option |
+minimap2-lr-hq |
+minimap2 with '-x lr:hq' option |
+
+
minimap2-no-preset |
minimap2 with no '-x' option |
diff --git a/docs/coverm-make.html b/docs/coverm-make.html
index 82360f2..c5ac44a 100644
--- a/docs/coverm-make.html
+++ b/docs/coverm-make.html
@@ -178,6 +178,10 @@ MAPPING ALGORITHM OPTIONS
minimap2 with '-x map-hifi' option |
+minimap2-lr-hq |
+minimap2 with '-x lr:hq' option |
+
+
minimap2-no-preset |
minimap2 with no '-x' option |
diff --git a/src/bam_generator.rs b/src/bam_generator.rs
index e428af9..5c1b953 100644
--- a/src/bam_generator.rs
+++ b/src/bam_generator.rs
@@ -51,6 +51,7 @@ pub enum MappingProgram {
MINIMAP2_ONT,
MINIMAP2_PB,
MINIMAP2_HIFI,
+ MINIMAP2_LR_HQ,
MINIMAP2_NO_PRESET,
STROBEALIGN,
}
@@ -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),
};
@@ -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",
@@ -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 => "",
}
)
diff --git a/src/bin/coverm.rs b/src/bin/coverm.rs
index 76fe0ca..1fa08e8 100644
--- a/src/bin/coverm.rs
+++ b/src/bin/coverm.rs
@@ -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");
@@ -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,
@@ -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();
}
diff --git a/src/cli.rs b/src/cli.rs
index a3839e2..bba577d 100644
--- a/src/cli.rs
+++ b/src/cli.rs
@@ -18,6 +18,7 @@ const MAPPING_SOFTWARE_LIST: &[&str] = &[
"minimap2-ont",
"minimap2-pb",
"minimap2-hifi",
+ "minimap2-lr-hq",
"minimap2-no-preset",
"strobealign",
];
@@ -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"))
diff --git a/src/coverage_printer.rs b/src/coverage_printer.rs
index 80b084e..b766a19 100644
--- a/src/coverage_printer.rs
+++ b/src/coverage_printer.rs
@@ -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);
diff --git a/src/mapping_index_maintenance.rs b/src/mapping_index_maintenance.rs
index 6b590f9..64f6c3f 100644
--- a/src/mapping_index_maintenance.rs
+++ b/src/mapping_index_maintenance.rs
@@ -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"),
};
@@ -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 => {
@@ -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
@@ -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);
@@ -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 => {}
};
diff --git a/src/mapping_parameters.rs b/src/mapping_parameters.rs
index 596d744..c762152 100644
--- a/src/mapping_parameters.rs
+++ b/src/mapping_parameters.rs
@@ -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."
@@ -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",
};
@@ -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
}
}
}
diff --git a/tests/test_cmdline.rs b/tests/test_cmdline.rs
index 50752ab..b89f95c 100644
--- a/tests/test_cmdline.rs
+++ b/tests/test_cmdline.rs
@@ -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