add qualities test & update README

README.md

@@ -31,6 +31,7 @@ use rust_spoa::poa_consensus;
 
 fn main() {
     let mut seqs = vec![];
+    let mut quals = vec![];
 
     // generated each string by adding small tweaks to the expected consensus "AATGCCCGTT"
     for seq in ["ATTGCCCGTT\0",

src/lib.rs

@@ -232,6 +232,37 @@ mod tests {
 
     }
 
+    #[test]
+    fn test_qualitites() {
+        let mut seqs = vec![];
+        let mut quals = vec![];
+
+        // expect consensus "FNLKPSWDDCQ"
+        for seq in [
+            "ATTGCCCATT\0".to_string(),
+            "ATTGCCCGTT\0".to_string(),
+            "ATTGCCCATT\0".to_string(),
+            "ATTGCCCGTT\0".to_string(),
+        ].iter() {
+            seqs.push(seq.chars().into_iter().map(|x|{x as u8}).collect::<Vec<u8>>());
+        }
+
+        for qual in [
+            "FFFFFFFIFF\0".to_string(),
+            "FFFFFFF#FF\0".to_string(),
+            "FFFFFFFIFF\0".to_string(),
+            "FFFFFFF#FF\0".to_string(),
+        ].iter() {
+            quals.push(qual.chars().into_iter().map(|x|{x as u8}).collect::<Vec<u8>>());
+        }
+
+        let consensus = poa_consensus(&seqs, &quals, 1, 5, -4, -3, -1, -3, -1);
+        eprintln!("{:?}", &consensus);
+
+        let expected = "ATTGCCCATT";
+        assert_eq!(consensus, expected);
+    }
+
     #[test]
     #[should_panic]
     fn test_not_null_terminated() {

src/poa_func.h

@@ -7,13 +7,13 @@ extern "C" {
 unsigned poa_func(char** seqs,  // the sequences (null-terminated) to perform multiple-sequence-alignment with.
                   char** quals, // the sequences (null-terminated) to perform multiple-sequence-alignment with.
                   int num_seqs, // the number of sequences being multiply aligned
-                  int l,        // the alignment type: 0 = local align, 1 = global align, 2 = semi-global
-                  int m,        // the score to give a sequence match in alignment, e.g. 5
-                  int n,        // the score to give a sequence mismatch in alignment, e.g. -4
-                  int g,        // the score to give a sequence gap in alignment, e.g. -3
-                  int e,        // the score to give a sequence gap extension in alignment, e.g. -1
-                  int q,        // the score to give a sequence second gap in alignment, e.g. -3
-                  int c,        // the score to give a sequence second gap extension in alignment, e.g. -1
+                  int l,        // alignment mode: 0 = local align, 1 = global align, 2 = semi-global
+                  int m,        // score for matching bases, e.g. 5
+                  int n,        // score for mismatching bases, e.g. -4
+                  int g,        // gap opening penalty (must be non-positive), e.g. -3
+                  int e,        // gap extension penalty (must be non-positivie), e.g. -1
+                  int q,        // gap opening penalty of the second affine function (must be non-positivie), e.g. -3
+                  int c,        // gap extension penalty of the second affine function (must be non-positivie), e.g. -1
                   );