Merge pull request #37 from rust-bio/improve-cigar-api

More improvements to CIGAR API.

Author: johanneskoester

CHANGELOG.md

@@ -2,6 +2,11 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.11.0] - 2017-05-1
+### Changed
+- Improved CIGAR string API using a newtype wrapper.
+
+
 ## [0.10.0] - 2016-11-10
 ### Added
 - Prelude module to easily import all relevant traits.

src/bam/record.rs

@@ -87,7 +87,7 @@ impl Record {
         self.inner_mut().core.pos = pos;
     }
 
-    pub fn end_pos(&self, cigar: &[Cigar]) -> i32 {
+    pub fn end_pos(&self, cigar: &CigarString) -> i32 {
         let mut pos = self.pos();
         for c in cigar {
             match c {
@@ -174,7 +174,7 @@ impl Record {
     }
 
     /// Set variable length data (qname, cigar, seq, qual).
-    pub fn set(&mut self, qname: &[u8], cigar: &[Cigar], seq: &[u8], qual: &[u8]) {
+    pub fn set(&mut self, qname: &[u8], cigar: &CigarString, seq: &[u8], qual: &[u8]) {
         self.inner_mut().l_data = (qname.len() + 1 + cigar.len() * 4 + ((seq.len() as f32 / 2.0).ceil() as usize) + qual.len()) as i32;
 
         if self.inner().m_data < self.inner().l_data {
@@ -552,6 +552,7 @@ custom_derive! {
     #[derive(NewtypeDeref,
              NewtypeIndex(usize),
              NewtypeIndexMut(usize),
+             NewtypeFrom,
              PartialEq,
              Eq,
              NewtypeDebug,
@@ -561,6 +562,13 @@ custom_derive! {
 }
 
 
+impl<'a> CigarString {
+    pub fn iter(&'a self) -> ::std::slice::Iter<'a, Cigar> {
+        self.into_iter()
+    }
+}
+
+
 impl<'a> IntoIterator for &'a CigarString {
     type Item = &'a Cigar;
     type IntoIter = ::std::slice::Iter<'a, Cigar>;