remove_minimap2_duplicated_headers: Use it.

See lh3/minimap2#527

.travis.yml

@@ -37,5 +37,5 @@ env:
 build: false
 
 test_script:
-- cargo test
+- PATH=target/debug:$PATH cargo test
 

src/bam_generator.rs

@@ -797,7 +797,7 @@ pub fn build_mapping_command(
     };
 
     return format!(
-        "{} {} -t {} {} '{}' {}",
+        "{} {} -t {} {} '{}' {}{}",
         match mapping_program {
             MappingProgram::BWA_MEM => "bwa mem".to_string(),
             _ => {
@@ -820,5 +820,11 @@ pub fn build_mapping_command(
         threads,
         read_params1,
         reference,
-        read_params2)
+        read_params2,
+        match mapping_program {
+            MappingProgram::BWA_MEM => {""},
+            // Required because of https://github.com/lh3/minimap2/issues/527
+            _ => " | remove_minimap2_duplicated_headers"
+        }
+    )
 }

src/bin/remove_minimap2_duplicated_headers.rs

@@ -12,6 +12,8 @@ fn main() {
     // @SQ lines before the @PG line are removed. Other lines are printed to
     // STDOUT.
 
+    // See https://github.com/lh3/minimap2/issues/527
+
     let mut is_before_pg = true;
 
     let stdin = std::io::stdin();