Add rammap as a supported read mapping program

.github/workflows/test-coverm.yml

@@ -84,7 +84,7 @@ jobs:
 
       - name: Run tests with Pixi
         run: |
-          pixi run --frozen cargo test -- --skip bwa_mem2 --skip strobealign
+          pixi run --frozen cargo test -- --skip bwa_mem2 --skip strobealign --skip rammap
 
   # Run after removing lock file so dependences are unlocked
   pixi_test_dependencies_optimistic_osx:
@@ -117,4 +117,4 @@ jobs:
 
       - name: Run tests with Pixi
         run: |
-          pixi run cargo test -- --skip bwa_mem2 --skip strobealign
+          pixi run cargo test -- --skip bwa_mem2 --skip strobealign --skip rammap

README.md

@@ -89,6 +89,7 @@ and one of these for mapping:
 * [strobealign](https://github.com/ksahlin/StrobeAlign) v0.14.0
 * [minimap2](https://github.com/lh3/minimap2) v2.21
 * [bwa-mem2](https://github.com/bwa-mem2/bwa-mem2) v2.0
+* [rammap](https://github.com/jwanglab/rammap) v1.1.1
 
 and one of these for genome dereplication:
 * [skani](https://github.com/bluenote-1577/skani) v0.1.1

pixi.toml

@@ -28,6 +28,7 @@ extern = "*"
 bwa-mem2 = "*"
 dashing = ">=0.4.0,<1.0"  # dashing 1.0 build gives illegal instruction errors
 strobealign = ">=0.14.0"  # tests generate the strobealign index at runtime
+rammap = ">=1.1.1"
 
 [package]
 name = "coverm"

src/bam_generator.rs

@@ -54,6 +54,7 @@ pub enum MappingProgram {
     MINIMAP2_LR_HQ,
     MINIMAP2_NO_PRESET,
     STROBEALIGN,
+    RAMMAP,
 }
 
 pub struct BamFileNamedReader {
@@ -416,7 +417,10 @@ 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::RAMMAP => None,
         // Required because of https://github.com/lh3/minimap2/issues/527
         MappingProgram::MINIMAP2_SR
         | MappingProgram::MINIMAP2_ONT
@@ -867,13 +871,21 @@ pub fn build_mapping_command(
     mapping_options: Option<&str>,
 ) -> String {
     let read_params1 = match mapping_program {
-        // minimap2 auto-detects interleaved based on read names
+        // minimap2 auto-detects interleaved input based on read names
         MappingProgram::MINIMAP2_SR
         | MappingProgram::MINIMAP2_ONT
         | MappingProgram::MINIMAP2_HIFI
         | MappingProgram::MINIMAP2_PB
         | MappingProgram::MINIMAP2_LR_HQ
         | MappingProgram::MINIMAP2_NO_PRESET => "",
+        MappingProgram::RAMMAP => match read_format {
+            // rammap's `sr` preset turns on fragment mode, which pulls read
+            // pairs from a single input file (this is how it maps interleaved
+            // reads). For genuinely single-end reads that would incorrectly
+            // consume the file as interleaved pairs, so disable fragment mode.
+            ReadFormat::Single => "--frag no",
+            ReadFormat::Coupled | ReadFormat::Interleaved => "",
+        },
         MappingProgram::BWA_MEM | MappingProgram::BWA_MEM2 => match read_format {
             ReadFormat::Interleaved => "-p",
             ReadFormat::Coupled | ReadFormat::Single => "",
@@ -896,6 +908,9 @@ 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(),
+            // rammap is a minimap2-compatible aligner; map short reads with
+            // the 'sr' preset and emit SAM with -a.
+            MappingProgram::RAMMAP => "rammap -x sr -a".to_string(),
             _ => {
                 let split_prefix = tempfile::Builder::new()
                     .prefix("coverm-minimap2-split-index")
@@ -915,7 +930,8 @@ pub fn build_mapping_command(
                     match mapping_program {
                         MappingProgram::BWA_MEM
                         | MappingProgram::BWA_MEM2
-                        | MappingProgram::STROBEALIGN => unreachable!(),
+                        | MappingProgram::STROBEALIGN
+                        | MappingProgram::RAMMAP => unreachable!(),
                         MappingProgram::MINIMAP2_SR => "-x sr",
                         MappingProgram::MINIMAP2_ONT => "-x map-ont",
                         MappingProgram::MINIMAP2_HIFI => "-x map-hifi",

src/bin/coverm.rs

@@ -800,6 +800,13 @@ fn setup_mapping_index(
                 )
             }
         }
+        MappingProgram::RAMMAP => {
+            // Pre-generating an index for a batch of readsets is not supported for rammap
+            info!("Not pre-generating rammap index");
+            Box::new(coverm::mapping_index_maintenance::VanillaIndexStruct::new(
+                reference_wise_params.reference,
+            ))
+        }
         MappingProgram::STROBEALIGN => {
             // Indexing once for a batch of readsets is not yet supported for strobealign
             info!("Not pre-generating strobealign index");
@@ -881,6 +888,7 @@ fn parse_mapping_program(m: &clap::ArgMatches) -> MappingProgram {
         Some("minimap2-lr-hq") => MappingProgram::MINIMAP2_LR_HQ,
         Some("minimap2-no-preset") => MappingProgram::MINIMAP2_NO_PRESET,
         Some("strobealign") => MappingProgram::STROBEALIGN,
+        Some("rammap") => MappingProgram::RAMMAP,
         None => DEFAULT_MAPPING_SOFTWARE_ENUM,
         _ => panic!(
             "Unexpected definition for --mapper: {:?}",
@@ -905,6 +913,9 @@ fn parse_mapping_program(m: &clap::ArgMatches) -> MappingProgram {
         MappingProgram::STROBEALIGN => {
             external_command_checker::check_for_strobealign();
         }
+        MappingProgram::RAMMAP => {
+            external_command_checker::check_for_rammap();
+        }
     }
     mapping_program
 }

src/cli.rs

@@ -21,6 +21,7 @@ const MAPPING_SOFTWARE_LIST: &[&str] = &[
     "minimap2-lr-hq",
     "minimap2-no-preset",
     "strobealign",
+    "rammap",
 ];
 const DEFAULT_MAPPING_SOFTWARE: &str = "strobealign";
 
@@ -94,6 +95,10 @@ fn add_mapping_options(manual: Manual) -> Manual {
                         &monospace_roff("minimap2-no-preset"),
                         &format!("minimap2 with no '{}' option", &monospace_roff("-x"))
                     ],
+                    &[
+                        &monospace_roff("rammap"),
+                        &format!("rammap (a minimap2-compatible aligner) with '{}' option", &monospace_roff("-x sr"))
+                    ],
                 ])
             )))
             .option(Opt::new("PARAMS").long("--minimap2-params").help(&format!(
@@ -120,6 +125,13 @@ fn add_mapping_options(manual: Manual) -> Manual {
         implications if untrusted input is specified. \
         [default: none]",
             ))
+            .option(Opt::new("PARAMS").long("--rammap-params").help(&format!(
+                "Extra parameters to provide to rammap. Note \
+        that usage of this parameter has security \
+        implications if untrusted input is specified. '{}' \
+        is always specified to rammap. [default: none]",
+                &monospace_roff("-x sr -a")
+            )))
             .flag(Flag::new().long("--strobealign-use-index").help(
                 "Use a pregenerated index (one that has been created with 'strobealign --create-index'). The --reference option should be specified as the original FASTA file i.e. 'ref.fna' not 'ref.fna.r100.sti' [default: not set]",
             )),
@@ -1244,6 +1256,13 @@ Ben J. Woodcroft <benjwoodcroft near gmail.com>
                         .requires("reference")
                         .action(clap::ArgAction::SetTrue),
                 )
+                .arg(
+                    Arg::new("rammap-params")
+                        .long("rammap-params")
+                        .long("rammap-parameters")
+                        .allow_hyphen_values(true)
+                        .requires("reference"),
+                )
                 // TODO: Relax this for autoconcatenation
                 .arg(
                     Arg::new("discard-unmapped")
@@ -1779,6 +1798,13 @@ Ben J. Woodcroft <benjwoodcroft near gmail.com>
                         .requires("reference")
                         .action(clap::ArgAction::SetTrue),
                 )
+                .arg(
+                    Arg::new("rammap-params")
+                        .long("rammap-params")
+                        .long("rammap-parameters")
+                        .allow_hyphen_values(true)
+                        .requires("reference"),
+                )
                 .arg(
                     Arg::new("discard-unmapped")
                         .long("discard-unmapped")
@@ -2156,6 +2182,13 @@ Ben J. Woodcroft <benjwoodcroft near gmail.com>
                         .long("strobealign-use-index")
                         .requires("reference")
                         .action(clap::ArgAction::SetTrue),
+                )
+                .arg(
+                    Arg::new("rammap-params")
+                        .long("rammap-params")
+                        .long("rammap-parameters")
+                        .allow_hyphen_values(true)
+                        .requires("reference"),
                 ),
         )
         .subcommand(

src/external_command_checker.rs

@@ -30,3 +30,10 @@ 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_rammap() {
+    check_for_external_command_presence_with_which("rammap")
+        .expect("Failed to find installed rammap");
+    default_version_check("rammap", "1.1.1", false, None)
+        .expect("Failed to find sufficient version of rammap");
+}

src/mapping_index_maintenance.rs

@@ -68,6 +68,7 @@ impl TemporaryIndexStruct {
             | MappingProgram::MINIMAP2_LR_HQ
             | MappingProgram::MINIMAP2_NO_PRESET => std::process::Command::new("minimap2"),
             MappingProgram::STROBEALIGN => std::process::Command::new("strobealign"),
+            MappingProgram::RAMMAP => std::process::Command::new("rammap"),
         };
         match &mapping_program {
             MappingProgram::BWA_MEM | MappingProgram::BWA_MEM2 => {
@@ -101,7 +102,8 @@ impl TemporaryIndexStruct {
                     MappingProgram::MINIMAP2_NO_PRESET
                     | MappingProgram::BWA_MEM
                     | MappingProgram::BWA_MEM2
-                    | MappingProgram::STROBEALIGN => {}
+                    | MappingProgram::STROBEALIGN
+                    | MappingProgram::RAMMAP => {}
                 };
                 if let Some(t) = num_threads {
                     cmd.arg("-t").arg(format!("{t}"));
@@ -111,6 +113,9 @@ impl TemporaryIndexStruct {
             MappingProgram::STROBEALIGN => {
                 warn!("STROBEALIGN pre-indexing is not supported currently, so skipping index generation.");
             }
+            MappingProgram::RAMMAP => {
+                warn!("RAMMAP pre-indexing is not supported currently, so skipping index generation.");
+            }
         };
         if let Some(params) = index_creation_options {
             for s in params.split_whitespace() {
@@ -207,7 +212,8 @@ pub fn check_reference_existence(reference_path: &str, mapping_program: &Mapping
         | MappingProgram::MINIMAP2_PB
         | MappingProgram::MINIMAP2_LR_HQ
         | MappingProgram::MINIMAP2_NO_PRESET
-        | MappingProgram::STROBEALIGN => {}
+        | MappingProgram::STROBEALIGN
+        | MappingProgram::RAMMAP => {}
     };
 
     if !ref_path.exists() {

src/mapping_parameters.rs

@@ -125,6 +125,7 @@ impl<'a> MappingParameters<'a> {
             | MappingProgram::MINIMAP2_LR_HQ
             | MappingProgram::MINIMAP2_NO_PRESET => "minimap2-params",
             MappingProgram::STROBEALIGN => "strobealign-params",
+            MappingProgram::RAMMAP => "rammap-params",
         };
         let mapping_options = match m.contains_id(mapping_parameters_arg) {
             true => {

tests/test_cmdline.rs

@@ -3239,6 +3239,55 @@ genome6~random_sequence_length_11003	0	0	0
             .is_file());
     }
 
+    #[test]
+    fn test_make_rammap() {
+        let td = tempfile::TempDir::new().unwrap();
+        Assert::main_binary()
+            .with_args(&[
+                "make",
+                "--coupled",
+                "tests/data/reads_for_seq1_and_seq2.1.fq.gz",
+                "tests/data/reads_for_seq1_and_seq2.2.fq.gz",
+                "--reference",
+                "tests/data/7seqs.fna",
+                "--mapper",
+                "rammap",
+                "--output-directory",
+                td.path().to_str().unwrap(),
+            ])
+            .succeeds()
+            .unwrap();
+        assert!(td
+            .path()
+            .join("7seqs.fna.reads_for_seq1_and_seq2.1.fq.gz.bam")
+            .is_file());
+    }
+
+    #[test]
+    fn test_make_rammap_single() {
+        // Single-end reads must not be consumed as interleaved pairs by
+        // rammap's fragment mode; exercise the single-end path end to end.
+        let td = tempfile::TempDir::new().unwrap();
+        Assert::main_binary()
+            .with_args(&[
+                "make",
+                "--single",
+                "tests/data/reads_for_seq1_and_seq2.1.fq.gz",
+                "--reference",
+                "tests/data/7seqs.fna",
+                "--mapper",
+                "rammap",
+                "--output-directory",
+                td.path().to_str().unwrap(),
+            ])
+            .succeeds()
+            .unwrap();
+        assert!(td
+            .path()
+            .join("7seqs.fna.reads_for_seq1_and_seq2.1.fq.gz.bam")
+            .is_file());
+    }
+
     #[test]
     fn test_strobealign_pregenerated_index() {
         // Generate the index at runtime so the format always matches the installed strobealign version