fix memory leaks, add rerun-if

Cargo.toml

@@ -13,4 +13,4 @@ failure = "*"
 [build-dependencies]
 cc = "^1.0"
 fs-utils = "*"
-
+glob = "^0.3"

build.rs

@@ -1,27 +1,24 @@
 // Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
 
 use fs_utils::copy::copy_directory;
+use glob::glob;
 use std::env;
 use std::path::Path;
 use std::process::Command;
 
 fn libcxx() -> &'static str {
     match env::var("CXX") {
-        Ok(cxx) => {
-            match Path::new(&cxx).file_name().unwrap().to_str().unwrap() {
-                s if s.contains("clang++") => "c++",
-                s if s.contains("g++") => "stdc++",
-                s => panic!("unknown compiler: {}", s),
-            }
-        }
-        Err(_) => {
-            match env::var("TARGET") {
-                Ok(ref s) if s.contains("darwin") => "c++",
-                Ok(ref s) if s.contains("linux") => "stdc++",
-                Ok(ref s) => panic!("unknown target: {}", s),
-                Err(_) => panic!("TARGET is undefined"),
-            }
-        }
+        Ok(cxx) => match Path::new(&cxx).file_name().unwrap().to_str().unwrap() {
+            s if s.contains("clang++") => "c++",
+            s if s.contains("g++") => "stdc++",
+            s => panic!("unknown compiler: {}", s),
+        },
+        Err(_) => match env::var("TARGET") {
+            Ok(ref s) if s.contains("darwin") => "c++",
+            Ok(ref s) if s.contains("linux") => "stdc++",
+            Ok(ref s) => panic!("unknown target: {}", s),
+            Err(_) => panic!("TARGET is undefined"),
+        },
     }
 }
 
@@ -48,7 +45,8 @@ fn main() {
         .arg("liborbit.a")
         .status()
         .unwrap()
-        .success() != true
+        .success()
+        != true
     {
         panic!("failed to build STAR");
     }
@@ -62,4 +60,14 @@ fn main() {
     println!("cargo:rustc-link-search=native={}", &out);
     println!("cargo:rustc-link-lib=static=orbit");
     println!("cargo:rustc-link-lib=dylib={}", libcxx());
+
+    // so we don't rebuild every time
+    for star_source in glob("STAR/source/**/*").expect("error in glob(STAR/source)") {
+        let star_source = star_source
+            .as_ref()
+            .expect("error in glob(STAR/source)")
+            .to_str()
+            .expect("STAR source could not be made into valid unicode");
+        println!("cargo:rerun-if-changed={}", star_source);
+    }
 }

src/lib.rs

@@ -63,6 +63,11 @@ impl StarReference {
 
         let reference = unsafe { bindings::init_star_ref(length, c_args) };
 
+        // recover stray CStrings to prevent leaked memory
+        nvec.into_iter().for_each(|ptr| unsafe {
+            CString::from_raw(ptr);
+        });
+
         let inner = InnerStarReference {
             reference,
             header,
@@ -423,17 +428,15 @@ mod test {
         println!("{:?}", recs);
     }
 
-
     #[test]
     fn test_multithreaded_alignment() {
-
         let settings = StarSettings::new(ERCC_REF);
         let reference = StarReference::load(settings).unwrap();
         let mut aligner1 = reference.get_aligner();
         let mut aligner2 = reference.get_aligner();
 
         let t1 = std::thread::spawn(move || {
-            for _ in 0 .. 100000 {
+            for _ in 0..100000 {
                 let recs = aligner1.align_read(NAME, ERCC_READ_1, ERCC_QUAL_1);
                 assert_eq!(recs.len(), 1);
                 assert_eq!(recs[0].pos(), 50);
@@ -442,7 +445,7 @@ mod test {
         });
 
         let t2 = std::thread::spawn(move || {
-            for _ in 0 .. 100000 {
+            for _ in 0..100000 {
                 let recs = aligner2.align_read(NAME, ERCC_READ_2, ERCC_QUAL_2);
                 assert_eq!(recs.len(), 1);
                 assert_eq!(recs[0].pos(), 500);
@@ -454,7 +457,6 @@ mod test {
         assert!(t2.join().is_ok());
     }
 
-
     #[test]
     #[ignore]
     fn test_align_read() {
@@ -520,7 +522,9 @@ mod test {
         let reference = StarReference::load(settings).unwrap();
         let mut aligner = reference.get_aligner();
 
-        let mut out = bam::Writer::from_path(&"test/test.bam", &reference.header(), bam::Format::BAM).unwrap();
+        let mut out =
+            bam::Writer::from_path(&"test/test.bam", &reference.header(), bam::Format::BAM)
+                .unwrap();
         let read = b"GTGCGGGGAGAAGTTTCAAGAAGGTTCTTATGGAAAAAAGGCTGTGAGCATAGAAAGCAGTCATAGGAGGTTGGGGAACTAGCTTGTCCCTCCCCACC";
         let qual = b"GGGAGIGIIIGIIGGGGIIGGIGGAGGAGGAAG.GGIIIG<AGGAGGGIGGGGIIIIIGGIGGGGGIGIIGGAGGGGGIGGGIGIIGGGGIIGGGIIG";
         let name = b"gatactaga";