Updated readme with fixed examples.

README.md

@@ -27,50 +27,60 @@ If you only want to use the library, there is no need to clone the repository. G
 To use Rust-HTSlib in your Rust project, import the crate from your source code:
 
 ```rust
-extern crate rust_htslib as htslib;
-use htslib::bam;
+extern crate rust_htslib;
 ```
 
 Rust-HTSlib provides a high level BAM API.
 Reading and writing BAM files is as easy as
+
 ```rust
-let bam = bam::Reader::new("path/to/some.bam").ok().expect("Error opening bam.");
-let out = bam::Writer::with_template("path/to/some.bam", "reversereads.bam").ok().expect("Error opening bam.");
+use rust_htslib::bam;
+use rust_htslib::bam::Read;
+
+let bam = bam::Reader::new(&"test/test.bam").ok().expect("Error opening bam.");
+let mut out = bam::Writer::with_template(&"test/test.bam", &"test/out.bam").ok().expect("Error opening bam.");
 
 // copy reverse reads to new BAM file
 for r in bam.records() {
     let record = r.ok().expect("Error reading BAM file.");
     if record.is_reverse() {
-        out.write(record);
+        out.write(&record).ok().expect("Error writing BAM file.");
     }
 }
 ```
 
 Pileups can be performed with
+
 ```rust
-let bam = bam::Reader::new("path/to/some.bam").ok().expect("Error opening bam.");
+use rust_htslib::bam;
+use rust_htslib::bam::Read;
+
+let bam = bam::Reader::new(&"test/test.bam").ok().expect("Error opening bam.");
 
 // pileup over all covered sites
 for p in bam.pileup() {
-    let pileup = p.ok().expect("Error reading BAM file.");
-    println!("{}:{} depth {}", bam.pileup.tid(), pileup.pos(), pileup.depth());
-
-    for alignment in pileup.alignments() {
-        match alignment.indel() {
-            bam::pileup::Indel::Ins(len) => println!("Insertion of length {}", len),
-            bam::pileup::Indel::Del(len) => println!("Deletion of length {}", len),
-            _ => println!("Base {}", alignment.record.seq()[alignment.qpos()])
-        }
-    }
+ let pileup = p.ok().expect("Error reading BAM file.");
+ println!("{}:{} depth {}", pileup.tid(), pileup.pos(), pileup.depth());
+
+ for alignment in pileup.alignments() {
+     match alignment.indel() {
+         bam::pileup::Indel::Ins(len) => println!("Insertion of length {}", len),
+         bam::pileup::Indel::Del(len) => println!("Deletion of length {}", len),
+         _ => println!("Base {}", alignment.record().seq()[alignment.qpos()])
+     }
+ }
 }
 ```
 In both cases, indexed BAM files can be seeked for specific regions, constraining either the record iterator or the pileups:
 
 ```rust
-let bam = bam::IndexedReader::new("path/to/some.bam");
+use rust_htslib::bam;
+
+let mut bam = bam::IndexedReader::new(&"test/test.bam").ok().expect("Error opening indexed BAM.");
 
 // seek to chr1:50000-100000
-bam.seek(bam.header.tid(b"chr1"), 50000, 100000).ok().expect("Error seeking BAM file.");
+let tid = bam.header.tid(b"CHROMOSOME_I").unwrap();
+bam.seek(tid, 0, 20).ok().expect("Error seeking BAM file.");
 // afterwards, read or pileup in this region
 ```