Merge pull request #21 from rust-bio/typed-constructors

Use properly typed parameters for constructing readers and writers.

Author: johanneskoester

.travis.yml

@@ -5,4 +5,5 @@ rust:
   - nightly
 env:
   global:
-    secure: ioWAhmR9VNa96Zn3UvY46bzys5LY6rHezT/nxsX6Wc0tZ3s/pk45wRKl9mU+oX+29EXMl2EXZZzsUlmY9AWNS34uQdBJ5HB68k2l2Cl44f/R4fQiFbkucCaCuTLDDshRsQInHTrsIjiB0tvjCG1tkNWQlgDIB4yeqPcL+YrmeMs=
+    - secure: ioWAhmR9VNa96Zn3UvY46bzys5LY6rHezT/nxsX6Wc0tZ3s/pk45wRKl9mU+oX+29EXMl2EXZZzsUlmY9AWNS34uQdBJ5HB68k2l2Cl44f/R4fQiFbkucCaCuTLDDshRsQInHTrsIjiB0tvjCG1tkNWQlgDIB4yeqPcL+YrmeMs=
+    - RUST_BACKTRACE=1

CHANGELOG.md

@@ -2,6 +2,14 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.10.0] - 2016-11-10
+### Added
+- Prelude module to easily import all relevant traits.
+### Changed
+- fine-grained constructors for STDIN/STDOUT, paths and URLs
+- better template handling with bam files
+
+
 ## [0.9.0] - 2016-11-02
 ### Changed
 - improved genotype handling

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "rust-htslib"
-version = "0.9.0"
+version = "0.10.0"
 authors = ["Christopher Schröder <christopher.schroeder@tu-dortmund.de>", "Johannes Köster <johannes.koester@tu-dortmund.de>"]
 build = "build.rs"
 description = "This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files."
@@ -17,6 +17,7 @@ itertools = "=0.4.*"
 quick-error = "1.1.*"
 newtype_derive = "0.1.*"
 custom_derive = "0.1.*"
+url = "1.2.*"
 ieee754 = "0.1"
 lazy_static = "0.1.*"
 

src/bam/header.rs

@@ -3,6 +3,8 @@
 // This file may not be copied, modified, or distributed
 // except according to those terms.
 
+use bam::HeaderView;
+
 
 /// A BAM header.
 pub struct Header {
@@ -16,6 +18,10 @@ impl Header {
         Header { records: Vec::new() }
     }
 
+    pub fn from_template(header: &HeaderView) -> Self {
+        Header { records: vec![header.as_bytes().to_owned()] }
+    }
+
     /// Add a record to the header.
     pub fn push_record(&mut self, record: &HeaderRecord) -> &mut Self {
         self.records.push(record.to_bytes());