Using linear map for VCF header record key/value pairs.

Author: holtgrewe

Cargo.toml

@@ -23,6 +23,7 @@ lazy_static = "0.2"
 bitflags = "0.9"
 serde = { version = "^1", optional = true }
 regex = "0.2"
+linear-map = "1.2.0"
 
 [features]
 default = []

src/bcf/header.rs

@@ -9,6 +9,8 @@ use std::str;
 
 use htslib;
 
+use linear_map::LinearMap;
+
 pub type SampleSubset = Vec<i32>;
 
 custom_derive! {
@@ -195,30 +197,15 @@ impl Drop for Header {
 #[derive(Debug)]
 pub enum HeaderRecord {
     /// A `FILTER` header record.
-    Filter {
-        key: String,
-        key_value_pairs: Vec<(String, String)>,
-    },
+    Filter { key: String, values: LinearMap<String, String> },
     /// An `INFO` header record.
-    Info {
-        key: String,
-        key_value_pairs: Vec<(String, String)>,
-    },
+    Info { key: String, values: LinearMap<String, String> },
     /// A `FORMAT` header record.
-    Format {
-        key: String,
-        key_value_pairs: Vec<(String, String)>,
-    },
+    Format { key: String, values: LinearMap<String, String> },
     /// A `contig` header record.
-    Contig {
-        key: String,
-        key_value_pairs: Vec<(String, String)>,
-    },
+    Contig { key: String, values: LinearMap<String, String> },
     /// A structured header record.
-    Structured {
-        key: String,
-        key_value_pairs: Vec<(String, String)>,
-    },
+    Structured { key: String, values: LinearMap<String, String> },
     /// A generic, unstructured header record.
     Generic { key: String, value: String },
 }
@@ -375,22 +362,12 @@ impl HeaderView {
 
     /// Return structured `HeaderRecord`s.
     pub fn header_records(&self) -> Vec<HeaderRecord> {
-        fn parse_kv(rec: &htslib::bcf_hrec_t) -> Vec<(String, String)> {
-            let mut result: Vec<(String, String)> = Vec::new();
+        fn parse_kv(rec: &htslib::bcf_hrec_t) -> LinearMap<String, String> {
+            let mut result: LinearMap<String, String> = LinearMap::new();
             for i in 0_i32..(rec.nkeys) {
-                let key = unsafe {
-                    ffi::CStr::from_ptr(*rec.keys.offset(i as isize))
-                        .to_str()
-                        .unwrap()
-                        .to_string()
-                };
-                let value = unsafe {
-                    ffi::CStr::from_ptr(*rec.vals.offset(i as isize))
-                        .to_str()
-                        .unwrap()
-                        .to_string()
-                };
-                result.push((key, value));
+                let key = unsafe { ffi::CStr::from_ptr(*rec.keys.offset(i as isize)).to_str().unwrap().to_string() };
+                let value = unsafe { ffi::CStr::from_ptr(*rec.vals.offset(i as isize)).to_str().unwrap().to_string() };
+                result.insert(key, value);
             }
             result
         }
@@ -402,23 +379,23 @@ impl HeaderView {
             let record = match rec.type_ {
                 0 => HeaderRecord::Filter {
                     key,
-                    key_value_pairs: parse_kv(rec),
+                    values: parse_kv(rec),
                 },
                 1 => HeaderRecord::Info {
                     key,
-                    key_value_pairs: parse_kv(rec),
+                    values: parse_kv(rec),
                 },
                 2 => HeaderRecord::Format {
                     key,
-                    key_value_pairs: parse_kv(rec),
+                    values: parse_kv(rec),
                 },
                 3 => HeaderRecord::Contig {
                     key,
-                    key_value_pairs: parse_kv(rec),
+                    values: parse_kv(rec),
                 },
                 4 => HeaderRecord::Structured {
                     key,
-                    key_value_pairs: parse_kv(rec),
+                    values: parse_kv(rec),
                 },
                 5 => HeaderRecord::Generic {
                     key,

src/bcf/mod.rs

@@ -850,10 +850,10 @@ mod tests {
         match &records[0] {
             &HeaderRecord::Filter {
                 ref key,
-                ref key_value_pairs,
+                ref values,
             } => {
                 assert_eq!(key, "FILTER");
-                assert_eq!(key_value_pairs[0], ("ID".to_string(), "PASS".to_string()));
+                assert_eq!(values["ID"], "PASS");
             }
             _ => {
                 assert!(false);

src/lib.rs

@@ -83,6 +83,8 @@ extern crate quick_error;
 extern crate regex;
 extern crate url;
 
+extern crate linear_map;
+
 #[cfg(feature = "serde")]
 extern crate serde;