From 6b7b70d7c11228aa1274eeac1f6ad1f646dd9fc4 Mon Sep 17 00:00:00 2001
From: Joseph Guhlin <joseph.guhlin@gmail.com>
Date: Fri, 22 Nov 2024 11:09:08 +1300
Subject: [PATCH] Integrate changes from #80

---
 Cargo.toml | 10 +++-------
 src/lib.rs | 10 +++++-----
 2 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index 6d5f8d6..6aa5f64 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "minimap2"
-version = "0.1.20+minimap2.2.28"
+version = "0.1.21+minimap2.2.28"
 edition = "2021"
 authors = ["Joseph Guhlin <joseph.guhlin@gmail.com>"]
 license = "MIT OR Apache-2.0"
@@ -24,15 +24,11 @@ exclude = [
 
 members = []
 
-exclude = [
-    "minimappers2",
-    "fakeminimap2",
-    "minimap2-sys"
-]
+exclude = ["minimappers2", "fakeminimap2", "minimap2-sys"]
 
 [dependencies]
 libc = "0.2"
-simdutf8 = {version = "0.1", optional = true}
+simdutf8 = { version = "0.1", optional = true }
 needletail = { version = "0.6", optional = true, default-features = false}
 
 # Dep for development
diff --git a/src/lib.rs b/src/lib.rs
index cc825d6..9da84f8 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -198,7 +198,7 @@ pub struct Alignment {
     pub cigar_str: Option<String>,
     pub md: Option<String>,
     pub cs: Option<String>,
-    pub alignment_score: Option<u32>,
+    pub alignment_score: Option<i32>,
 }
 
 /// Mapping result
@@ -782,12 +782,12 @@ impl Aligner {
     /// query_name: Name of the query sequence
     pub fn map(
         &self,
+        query_name: Option<&[u8]>,
         seq: &[u8],
         cs: bool,
         md: bool, // TODO
         max_frag_len: Option<usize>,
         extra_flags: Option<&[u64]>,
-        query_name: Option<&[u8]>,
     ) -> Result<Vec<Mapping>, &'static str> {
         // Make sure index is set
         if !self.has_index() {
@@ -847,8 +847,8 @@ impl Aligner {
                     let contig: *mut ::std::os::raw::c_char =
                         (*((*(self.idx.unwrap())).seq.offset(reg.rid as isize))).name;
 
-                    let is_primary = reg.parent == reg.id;
-                    let is_supplementary = reg.sam_pri() == 0;
+                    let is_primary = reg.parent == reg.id && (reg.sam_pri() > 0);
+                    let is_supplementary = (reg.parent == reg.id) && (reg.sam_pri() == 0);
 
                     // todo holy heck this code is ugly
                     let alignment = if !reg.p.is_null() {
@@ -989,7 +989,7 @@ impl Aligner {
                             cigar_str,
                             md: md_str,
                             cs: cs_str,
-                            alignment_score: Some(p.dp_score as u32),
+                            alignment_score: Some(p.dp_score as i32),
                         })
                     } else {
                         None