Use bwa-mem2 not bwa-mem.

Fixes #72.

Suggested by: @jianshu93.

.travis.yml

@@ -22,7 +22,7 @@ install:
   - conda config --add channels bioconda
   - conda config --add channels conda-forge
 
-  - conda create -q -n test-environment bwa 'samtools>=1.9' 'minimap2=2.17' 'dashing>=0.4.0' 'fastani>=1.3'
+  - conda create -q -n test-environment bwa-mem2 'samtools>=1.9' 'minimap2=2.17' 'dashing>=0.4.0' 'fastani>=1.3'
   - source activate test-environment
   - cargo build --verbose
 

README.md

@@ -75,7 +75,7 @@ For the full suite of options, these additional programs must be installed:
 
 and some mapping software:
 * [minimap2](https://github.com/lh3/minimap2) v2.17-r941 (2.18 will _not_ work)
-* [bwa](https://github.com/lh3/bwa) v0.7.17-r1188
+* [bwa-mem2](https://github.com/bwa-mem2/bwa-mem2) v2.0
 
 For dereplication:
 * [Dashing](https://github.com/dnbaker/dashing) v0.4.0

src/bam_generator.rs

@@ -948,7 +948,7 @@ pub fn build_mapping_command(
     return format!(
         "{} {} -t {} {} '{}' {}",
         match mapping_program {
-            MappingProgram::BWA_MEM => "bwa mem".to_string(),
+            MappingProgram::BWA_MEM => "bwa-mem2 mem".to_string(),
             _ => {
                 let split_prefix = tempfile::NamedTempFile::new().expect(&format!(
                     "Failed to create {:?} minimap2 split_prefix file",

src/external_command_checker.rs

@@ -1,7 +1,9 @@
 use bird_tool_utils::external_command_checker::*;
 
 pub fn check_for_bwa() {
-    check_for_external_command_presence("BWA", "which bwa").expect("Failed to find installed BWA");
+    check_for_external_command_presence("BWA", "which bwa-mem2").expect("Failed to find installed BWA");
+    default_version_check("bwa-mem2", "2.0", false, Some("bwa-mem2 version"))
+        .expect("Failed to find sufficient version of bwa-mem2");
 }
 
 pub fn check_for_minimap2() {

src/mapping_index_maintenance.rs

@@ -59,7 +59,7 @@ impl TemporaryIndexStruct {
             mapping_program, reference_path
         );
         let mut cmd = match mapping_program {
-            MappingProgram::BWA_MEM => std::process::Command::new("bwa"),
+            MappingProgram::BWA_MEM => std::process::Command::new("bwa-mem2"),
             MappingProgram::MINIMAP2_SR
             | MappingProgram::MINIMAP2_ONT
             | MappingProgram::MINIMAP2_PB
@@ -158,7 +158,7 @@ pub fn generate_bwa_index(
     reference_path: &str,
     index_creation_parameters: Option<&str>,
 ) -> Box<dyn MappingIndex> {
-    let bwa_extensions = vec!["amb", "ann", "bwt", "pac", "sa"];
+    let bwa_extensions = vec!["0123", "amb", "ann", "bwt.2bit.64", "pac"];
     let num_extensions = bwa_extensions.len();
     let mut num_existing: u8 = 0;
     for extension in bwa_extensions {