Merge branch 'master' into ar/header-remove-unwrap

.github/dependabot.yml

@@ -4,7 +4,3 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
-    commit-message:
-      # Prefix all commit messages with "deps: ", which should be
-      # accepted as a conventional commit and trigger release-please
-      prefix: "deps"

CHANGELOG.md

@@ -2,6 +2,18 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.48.0](https://github.com/rust-bio/rust-htslib/compare/v0.47.1...v0.48.0) (2024-11-12)
+
+
+### Features
+
+* Add to_vcf_string method for bcf::Record ([#443](https://github.com/rust-bio/rust-htslib/issues/443)) ([489c0d7](https://github.com/rust-bio/rust-htslib/commit/489c0d7677445cfe38580c8d4c843ad4f4e2d827))
+
+
+### Bug Fixes
+
+* return error when bgzf_open fails to open a file ([#444](https://github.com/rust-bio/rust-htslib/issues/444)) ([9bda5f7](https://github.com/rust-bio/rust-htslib/commit/9bda5f768a5c54767c7e08ef1cafd28ff3f2a3b3))
+
 ## [0.47.1](https://github.com/rust-bio/rust-htslib/compare/v0.47.0...v0.47.1) (2024-11-12)
 
 

Cargo.toml

@@ -9,7 +9,7 @@ license = "MIT"
 name = "rust-htslib"
 readme = "README.md"
 repository = "https://github.com/rust-bio/rust-htslib.git"
-version = "0.47.1"
+version = "0.48.0"
 
 [package.metadata.release]
 pre-release-commit-message = "release version {{version}}"
@@ -20,7 +20,7 @@ libz-sys = ">=1.1.15"
 bio-types = ">=0.9"
 byteorder = "1.3"
 custom_derive = "0.1"
-derive-new = "0.5"
+derive-new = "0.7"
 hts-sys = {version = "2.1.4", default-features = false, features = ["bindgen"]}
 ieee754 = "0.2"
 lazy_static = "1.4"
@@ -30,7 +30,7 @@ newtype_derive = "0.1"
 regex = "1.3"
 serde = {version = "^1", optional = true, features = ["derive"]}
 serde_bytes = {version = "0.11", optional = true}
-thiserror = "1"
+thiserror = "2"
 url = "2.1"
 
 [features]
@@ -47,6 +47,6 @@ static = ["hts-sys/static"]
 
 [dev-dependencies]
 bincode = "1.2"
-pretty_assertions = "0.6"
+pretty_assertions = "1.4"
 serde_json = "1.0"
 tempfile = "3.1.0"

src/bcf/record.rs

@@ -1088,6 +1088,38 @@ impl Record {
         }
         "".to_owned()
     }
+
+    /// Convert to VCF String
+    ///
+    /// Intended for debug only. Use Writer for efficient VCF output.
+    ///
+    pub fn to_vcf_string(&self) -> Result<String> {
+        let mut buf = htslib::kstring_t {
+            l: 0,
+            m: 0,
+            s: ptr::null_mut(),
+        };
+        let ret = unsafe { htslib::vcf_format(self.header().inner, self.inner, &mut buf) };
+
+        if ret < 0 {
+            if !buf.s.is_null() {
+                unsafe {
+                    libc::free(buf.s as *mut libc::c_void);
+                }
+            }
+            return Err(Error::BcfToString);
+        }
+
+        let vcf_str = unsafe {
+            let vcf_str = String::from(ffi::CStr::from_ptr(buf.s).to_str().unwrap());
+            if !buf.s.is_null() {
+                libc::free(buf.s as *mut libc::c_void);
+            }
+            vcf_str
+        };
+
+        Ok(vcf_str)
+    }
 }
 
 impl Clone for Record {
@@ -1714,4 +1746,30 @@ mod tests {
         assert!(!record.has_filter(&bar));
         assert!(record.has_filter("PASS".as_bytes()));
     }
+
+    #[test]
+    fn test_record_to_vcf_string_err() {
+        let tmp = NamedTempFile::new().unwrap();
+        let path = tmp.path();
+        let header = Header::new();
+        let vcf = Writer::from_path(path, &header, true, Format::Vcf).unwrap();
+        let record = vcf.empty_record();
+        assert!(record.to_vcf_string().is_err());
+    }
+
+    #[test]
+    fn test_record_to_vcf_string() {
+        let tmp = NamedTempFile::new().unwrap();
+        let path = tmp.path();
+        let mut header = Header::new();
+        header.push_record(b"##contig=<ID=chr1,length=1000>");
+        header.push_record(br#"##FILTER=<ID=foo,Description="sample is a foo fighter">"#);
+        let vcf = Writer::from_path(path, &header, true, Format::Vcf).unwrap();
+        let mut record = vcf.empty_record();
+        record.push_filter("foo".as_bytes()).unwrap();
+        assert_eq!(
+            record.to_vcf_string().unwrap(),
+            "chr1\t1\t.\t.\t.\t0\tfoo\t.\n"
+        );
+    }
 }

src/bgzf/mod.rs

@@ -87,7 +87,13 @@ impl Reader {
         let mode = ffi::CString::new("r").unwrap();
         let cpath = ffi::CString::new(path).unwrap();
         let inner = unsafe { htslib::bgzf_open(cpath.as_ptr(), mode.as_ptr()) };
-        Ok(Self { inner })
+        if inner != std::ptr::null_mut() {
+            Ok(Self { inner })
+        } else {
+            Err(Error::FileOpen {
+                path: String::from_utf8(path.to_vec()).unwrap(),
+            })
+        }
     }
 
     /// Set the thread pool to use for parallel decompression.
@@ -211,7 +217,13 @@ impl Writer {
         let mode = Self::get_open_mode(level)?;
         let cpath = ffi::CString::new(path).unwrap();
         let inner = unsafe { htslib::bgzf_open(cpath.as_ptr(), mode.as_ptr()) };
-        Ok(Self { inner, tpool: None })
+        if inner != std::ptr::null_mut() {
+            Ok(Self { inner, tpool: None })
+        } else {
+            Err(Error::FileOpen {
+                path: String::from_utf8(path.to_vec()).unwrap(),
+            })
+        }
     }
 
     /// Internal function to convert compression level to "mode"

src/errors.rs

@@ -10,6 +10,8 @@ pub enum Error {
     // General errors
     #[error("file not found: {path}")]
     FileNotFound { path: PathBuf },
+    #[error("file could not be opened: {path}")]
+    FileOpen { path: String },
     #[error("invalid (non-unicode) characters in path")]
     NonUnicodePath,
     #[error("failed to fetch region")]
@@ -131,6 +133,8 @@ pub enum Error {
     BcfSetValues,
     #[error("failed to remove alleles in BCF/VCF record")]
     BcfRemoveAlleles,
+    #[error("failed to render BCF record as string")]
+    BcfToString,
 
     #[error("invalid compression level {level}")]
     BgzfInvalidCompressionLevel { level: i8 },