Add x-mapper support

pixi.toml

@@ -21,6 +21,7 @@ bwa = ">=0.7.17"
 skani = ">=0.2.2"
 fastani = ">=1.3"
 extern = "*"
+x-mapper = "*"
 
 # x86_64-specific dependencies
 [target.linux-64.dependencies]

src/bam_generator.rs

@@ -53,6 +53,7 @@ pub enum MappingProgram {
     MINIMAP2_HIFI,
     MINIMAP2_NO_PRESET,
     STROBEALIGN,
+    X_MAPPER,
 }
 
 pub struct BamFileNamedReader {
@@ -415,7 +416,10 @@ pub fn generate_named_bam_readers_from_reads(
 
     // Required because of https://github.com/wwood/CoverM/issues/58
     let minimap2_log_file_index = match mapping_program {
-        MappingProgram::BWA_MEM | MappingProgram::BWA_MEM2 | MappingProgram::STROBEALIGN => None,
+        MappingProgram::BWA_MEM
+        | MappingProgram::BWA_MEM2
+        | MappingProgram::STROBEALIGN
+        | MappingProgram::X_MAPPER => None,
         // Required because of https://github.com/lh3/minimap2/issues/527
         MappingProgram::MINIMAP2_SR
         | MappingProgram::MINIMAP2_ONT
@@ -864,6 +868,32 @@ pub fn build_mapping_command(
     read2_path: Option<&str>,
     mapping_options: Option<&str>,
 ) -> String {
+    if matches!(mapping_program, MappingProgram::X_MAPPER) {
+        let read_params = match read_format {
+            ReadFormat::Coupled => format!(
+                "--paired-queries '{}' '{}'",
+                read1_path,
+                read2_path.unwrap()
+            ),
+            ReadFormat::Single => format!("--queries '{}'", read1_path),
+            ReadFormat::Interleaved => {
+                panic!("Interleaved reads are not supported by X-Mapper")
+            }
+        };
+        let mapping_options = mapping_options
+            .filter(|opts| !opts.is_empty())
+            .map(|opts| format!(" {opts}"))
+            .unwrap_or_default();
+        return format!(
+            "x-mapper{} --num-threads {} --reference '{}' {} --out-sam - | samtools calmd -S - '{}'",
+            mapping_options,
+            threads,
+            reference.index_path(),
+            read_params,
+            reference.index_path()
+        );
+    }
+
     let read_params1 = match mapping_program {
         // minimap2 auto-detects interleaved based on read names
         MappingProgram::MINIMAP2_SR
@@ -879,6 +909,7 @@ pub fn build_mapping_command(
             ReadFormat::Interleaved => "--interleaved",
             ReadFormat::Coupled | ReadFormat::Single => "",
         },
+        MappingProgram::X_MAPPER => unreachable!(),
     };
 
     let read_params2 = match read_format {
@@ -893,6 +924,7 @@ pub fn build_mapping_command(
             MappingProgram::BWA_MEM => "bwa mem".to_string(),
             MappingProgram::BWA_MEM2 => "bwa-mem2 mem".to_string(),
             MappingProgram::STROBEALIGN => "strobealign".to_string(),
+            MappingProgram::X_MAPPER => unreachable!(),
             _ => {
                 let split_prefix = tempfile::Builder::new()
                     .prefix("coverm-minimap2-split-index")
@@ -912,7 +944,8 @@ pub fn build_mapping_command(
                     match mapping_program {
                         MappingProgram::BWA_MEM
                         | MappingProgram::BWA_MEM2
-                        | MappingProgram::STROBEALIGN => unreachable!(),
+                        | MappingProgram::STROBEALIGN
+                        | MappingProgram::X_MAPPER => unreachable!(),
                         MappingProgram::MINIMAP2_SR => "-x sr",
                         MappingProgram::MINIMAP2_ONT => "-x map-ont",
                         MappingProgram::MINIMAP2_HIFI => "-x map-hifi",

src/bin/coverm.rs

@@ -820,6 +820,12 @@ fn setup_mapping_index(
                 ))
             }
         }
+        MappingProgram::X_MAPPER => {
+            info!("Not pre-generating x-mapper index");
+            Box::new(coverm::mapping_index_maintenance::VanillaIndexStruct::new(
+                reference_wise_params.reference,
+            ))
+        }
     }
 }
 
@@ -879,6 +885,7 @@ fn parse_mapping_program(m: &clap::ArgMatches) -> MappingProgram {
         Some("minimap2-hifi") => MappingProgram::MINIMAP2_HIFI,
         Some("minimap2-no-preset") => MappingProgram::MINIMAP2_NO_PRESET,
         Some("strobealign") => MappingProgram::STROBEALIGN,
+        Some("x-mapper") => MappingProgram::X_MAPPER,
         None => DEFAULT_MAPPING_SOFTWARE_ENUM,
         _ => panic!(
             "Unexpected definition for --mapper: {:?}",
@@ -902,6 +909,9 @@ fn parse_mapping_program(m: &clap::ArgMatches) -> MappingProgram {
         MappingProgram::STROBEALIGN => {
             external_command_checker::check_for_strobealign();
         }
+        MappingProgram::X_MAPPER => {
+            external_command_checker::check_for_x_mapper();
+        }
     }
     mapping_program
 }

src/cli.rs

@@ -20,6 +20,7 @@ const MAPPING_SOFTWARE_LIST: &[&str] = &[
     "minimap2-hifi",
     "minimap2-no-preset",
     "strobealign",
+    "x-mapper",
 ];
 const DEFAULT_MAPPING_SOFTWARE: &str = "strobealign";
 
@@ -86,11 +87,15 @@ fn add_mapping_options(manual: Manual) -> Manual {
                         &format!("minimap2 with '{}' option", &monospace_roff("-x map-hifi"))
                     ],
                     &[
-                        &monospace_roff("minimap2-no-preset"),
-                        &format!("minimap2 with no '{}' option", &monospace_roff("-x"))
-                    ],
-                ])
-            )))
+                    &monospace_roff("minimap2-no-preset"),
+                    &format!("minimap2 with no '{}' option", &monospace_roff("-x"))
+                ],
+                &[
+                    &monospace_roff("x-mapper"),
+                    "x-mapper using default parameters"
+                ],
+            ])
+        )))
             .option(Opt::new("PARAMS").long("--minimap2-params").help(&format!(
                 "Extra parameters to provide to minimap2, \
         both indexing command (if used) and for \
@@ -113,6 +118,12 @@ fn add_mapping_options(manual: Manual) -> Manual {
                 "Extra parameters to provide to strobealign. Note \
         that usage of this parameter has security \
         implications if untrusted input is specified. \
+        [default: none]",
+            ))
+            .option(Opt::new("PARAMS").long("--x-mapper-params").help(
+                "Extra parameters to provide to x-mapper. Note \
+        that usage of this parameter has security \
+        implications if untrusted input is specified. \
         [default: none]",
             ))
             .flag(Flag::new().long("--strobealign-use-index").help(
@@ -1233,6 +1244,13 @@ Ben J. Woodcroft <benjwoodcroft near gmail.com>
                         .allow_hyphen_values(true)
                         .requires("reference"),
                 )
+                .arg(
+                    Arg::new("x-mapper-params")
+                        .long("x-mapper-params")
+                        .long("x-mapper-parameters")
+                        .allow_hyphen_values(true)
+                        .requires("reference"),
+                )
                 .arg(
                     Arg::new("strobealign-use-index")
                         .long("strobealign-use-index")
@@ -1768,6 +1786,13 @@ Ben J. Woodcroft <benjwoodcroft near gmail.com>
                         .allow_hyphen_values(true)
                         .requires("reference"),
                 )
+                .arg(
+                    Arg::new("x-mapper-params")
+                        .long("x-mapper-params")
+                        .long("x-mapper-parameters")
+                        .allow_hyphen_values(true)
+                        .requires("reference"),
+                )
                 .arg(
                     Arg::new("strobealign-use-index")
                         .long("strobealign-use-index")
@@ -2146,6 +2171,13 @@ Ben J. Woodcroft <benjwoodcroft near gmail.com>
                         .allow_hyphen_values(true)
                         .requires("reference"),
                 )
+                .arg(
+                    Arg::new("x-mapper-params")
+                        .long("x-mapper-params")
+                        .long("x-mapper-parameters")
+                        .allow_hyphen_values(true)
+                        .requires("reference"),
+                )
                 .arg(
                     Arg::new("strobealign-use-index")
                         .long("strobealign-use-index")

src/external_command_checker.rs

@@ -30,3 +30,8 @@ pub fn check_for_strobealign() {
     default_version_check("strobealign", "0.11.0", false, None)
         .expect("Failed to find sufficient version of strobealign");
 }
+
+pub fn check_for_x_mapper() {
+    check_for_external_command_presence_with_which("x-mapper")
+        .expect("Failed to find installed x-mapper");
+}

src/mapping_index_maintenance.rs

@@ -67,6 +67,7 @@ impl TemporaryIndexStruct {
             | MappingProgram::MINIMAP2_HIFI
             | MappingProgram::MINIMAP2_NO_PRESET => std::process::Command::new("minimap2"),
             MappingProgram::STROBEALIGN => std::process::Command::new("strobealign"),
+            MappingProgram::X_MAPPER => unreachable!(),
         };
         match &mapping_program {
             MappingProgram::BWA_MEM | MappingProgram::BWA_MEM2 => {
@@ -96,7 +97,8 @@ impl TemporaryIndexStruct {
                     MappingProgram::MINIMAP2_NO_PRESET
                     | MappingProgram::BWA_MEM
                     | MappingProgram::BWA_MEM2
-                    | MappingProgram::STROBEALIGN => {}
+                    | MappingProgram::STROBEALIGN
+                    | MappingProgram::X_MAPPER => {}
                 };
                 if let Some(t) = num_threads {
                     cmd.arg("-t").arg(format!("{t}"));
@@ -106,6 +108,9 @@ impl TemporaryIndexStruct {
             MappingProgram::STROBEALIGN => {
                 warn!("STROBEALIGN pre-indexing is not supported currently, so skipping index generation.");
             }
+            MappingProgram::X_MAPPER => {
+                warn!("X_MAPPER pre-indexing is not supported currently, so skipping index generation.");
+            }
         };
         if let Some(params) = index_creation_options {
             for s in params.split_whitespace() {
@@ -201,7 +206,8 @@ pub fn check_reference_existence(reference_path: &str, mapping_program: &Mapping
         | MappingProgram::MINIMAP2_HIFI
         | MappingProgram::MINIMAP2_PB
         | MappingProgram::MINIMAP2_NO_PRESET
-        | MappingProgram::STROBEALIGN => {}
+        | MappingProgram::STROBEALIGN
+        | MappingProgram::X_MAPPER => {}
     };
 
     if !ref_path.exists() {

src/mapping_parameters.rs

@@ -111,6 +111,14 @@ impl<'a> MappingParameters<'a> {
                     process::exit(1);
                 }
             }
+            MappingProgram::X_MAPPER => {
+                if !interleaved.is_empty() {
+                    error!(
+                        "Interleaved read input specified to be mapped with x-mapper which is not supported."
+                    );
+                    process::exit(1);
+                }
+            }
             _ => {}
         }
 
@@ -122,6 +130,7 @@ impl<'a> MappingParameters<'a> {
             | MappingProgram::MINIMAP2_PB
             | MappingProgram::MINIMAP2_NO_PRESET => "minimap2-params",
             MappingProgram::STROBEALIGN => "strobealign-params",
+            MappingProgram::X_MAPPER => "x-mapper-params",
         };
         let mapping_options = match m.contains_id(mapping_parameters_arg) {
             true => {