Make all HeaderView types cloneable.

Author: johanneskoester

CHANGELOG.md

@@ -2,7 +2,12 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
-## [0.14.0] - unreleased
+## [0.15.0] - 2017-12-05
+### Changed
+- HeaderView of bam and bcf can now be cloned.
+
+
+## [0.14.0] - 2017-12-03
 ### Added
 - An efficient ringbuffer for accessing BCF regions
 - An efficient ringbuffer for accessing BAM regions

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "rust-htslib"
-version = "0.14.0"
+version = "0.15.0"
 authors = ["Christopher Schröder <[email protected]>", "Johannes Köster <[email protected]>"]
 build = "build.rs"
 description = "This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files."

src/bcf/header.rs

@@ -172,6 +172,25 @@ impl HeaderView {
     }
 }
 
+
+impl Clone for HeaderView {
+    fn clone(&self) -> Self {
+        HeaderView {
+            inner: unsafe { htslib::vcf::bcf_hdr_dup(self.inner) }
+        }
+    }
+}
+
+
+impl Drop for HeaderView {
+    fn drop(&mut self) {
+        unsafe {
+            htslib::vcf::bcf_hdr_destroy(self.inner);
+        }
+    }
+}
+
+
 pub enum TagType {
     Flag,
     Integer,

src/bcf/mod.rs

@@ -22,7 +22,7 @@ pub use bcf::buffer::RecordBuffer;
 
 pub struct Reader {
     inner: *mut htslib::vcf::htsFile,
-    pub header: HeaderView,
+    header: HeaderView,
 }
 
 
@@ -56,6 +56,10 @@ impl Reader {
         Ok(Reader { inner: htsfile, header: HeaderView::new(header) })
     }
 
+    pub fn header(&self) -> &HeaderView {
+        &self.header
+    }
+
     pub fn read(&mut self, record: &mut record::Record) -> Result<(), ReadError> {
         match unsafe { htslib::vcf::bcf_read(self.inner, self.header.inner, record.inner) } {
             0  => {
@@ -76,7 +80,6 @@ impl Reader {
 impl Drop for Reader {
     fn drop(&mut self) {
         unsafe {
-            htslib::vcf::bcf_hdr_destroy(self.header.inner);
             htslib::vcf::hts_close(self.inner);
         }
     }
@@ -85,7 +88,7 @@ impl Drop for Reader {
 
 pub struct Writer {
     inner: *mut htslib::vcf::htsFile,
-    pub header: HeaderView,
+    header: HeaderView,
     subset: Option<SampleSubset>,
 }
 
@@ -127,6 +130,10 @@ impl Writer {
         })
     }
 
+    pub fn header(&self) -> &HeaderView {
+        &self.header
+    }
+
     /// Translate record to header of this writer.
     pub fn translate(&mut self, record: &mut record::Record) {
         unsafe {
@@ -159,7 +166,6 @@ impl Writer {
 impl Drop for Writer {
     fn drop(&mut self) {
         unsafe {
-            htslib::vcf::bcf_hdr_destroy(self.header.inner);
             htslib::vcf::hts_close(self.inner);
         }
     }

src/lib.rs

@@ -59,7 +59,7 @@
 //! let mut bam = bam::IndexedReader::from_path(&"test/test.bam").unwrap();
 //!
 //! // seek to chr1:50000-100000
-//! let tid = bam.header.tid(b"CHROMOSOME_I").unwrap();
+//! let tid = bam.header().tid(b"CHROMOSOME_I").unwrap();
 //! bam.fetch(tid, 0, 20).unwrap();
 //! // afterwards, read or pileup in this region
 //! ```