updated fN to real name

Author: nmmsv10x

Cargo.lock

@@ -209,7 +209,7 @@ fn main() {
         annotate_seq(&x, &refdata, &mut ann, true, false, true);
         let mut annv = Vec::<Annotation>::new();
         for i in 0..ann.len() {
-            let t = ann[i].f2 as usize;
+            let t = ann[i].ref_id as usize;
             if refdata.is_v(t) {
                 annv.push(ann[i]);
             }
@@ -255,7 +255,7 @@ fn main() {
             let mut v_ref_id = None;
             let mut j_ref_id = None;
             for i in 0..ann.len() {
-                let t = ann[i].f2 as usize;
+                let t = ann[i].ref_id as usize;
                 if refdata.is_v(t) {
                     v_ref_id = Some(t);
                 } else if refdata.is_j(t) {
@@ -325,8 +325,8 @@ fn main() {
                 let mut seq_start = vstart as isize;
                 // probably not exactly right
                 if annv.len() > 1 {
-                    let q1 = annv[0].f0 + ann[0].f1;
-                    let q2 = annv[1].f0;
+                    let q1 = annv[0].tig_start + ann[0].match_len;
+                    let q2 = annv[1].tig_start;
                     seq_start += q2 as isize - q1 as isize;
                 }
                 let mut seq_end = seq.len() - (jref.len() - jend);

enclone_paper/src/bin/olga_splice.rs

@@ -339,8 +339,8 @@ pub fn align_n(
                                 let mut seq_start = vstart as isize;
                                 // probably not exactly right
                                 if ex.share[r].annv.len() > 1 {
-                                    let q1 = ex.share[r].annv[0].f0 + ex.share[r].annv[0].f1;
-                                    let q2 = ex.share[r].annv[1].f0;
+                                    let q1 = ex.share[r].annv[0].tig_start + ex.share[r].annv[0].match_len;
+                                    let q2 = ex.share[r].annv[1].tig_start;
                                     seq_start += q2 as isize - q1 as isize;
                                 }
                                 let mut seq_end = seq.len() - (jref.len() - jend);

enclone_tail/src/align_n.rs

@@ -161,20 +161,20 @@ fn main() {
             let (mut v, mut j) = (None, None);
             let (mut vstart, mut jstop) = (0, 0);
             for i in 0..ann.len() {
-                let t = ann[i].f2 as usize;
+                let t = ann[i].ref_id as usize;
                 if refdata.rtype[t] == 0 as i32 || refdata.rtype[t] == 4 as i32 {
                     if refdata.is_v(t) {
                         v = Some(t);
                     } else if refdata.is_j(t) {
                         j = Some(t);
-                        jstop = (ann[i].f0 + ann[i].f1) as usize;
+                        jstop = (ann[i].tig_start + ann[i].match_len) as usize;
                     }
                 }
             }
             for i in 0..ann.len() {
-                let t = ann[i].f2 as usize;
+                let t = ann[i].ref_id as usize;
                 if refdata.is_v(t) {
-                    vstart = ann[i].f0 as usize;
+                    vstart = ann[i].tig_start as usize;
                     break;
                 }
             }

enclone_tools/src/bin/annotate_seq.rs

@@ -84,14 +84,14 @@ fn main() {
         let (valid, _) = is_productive_contig(&seq, &refdata, &ann);
         let mut shift = false;
         for i in 1..ann.len() {
-            if ann[i - 1].f2 == ann[i].f2 {
-                if ann[i].f0 == ann[i - 1].f0 + ann[i - 1].f1 + 1
-                    && ann[i].f3 == ann[i - 1].f3 + ann[i - 1].f1
+            if ann[i - 1].ref_id == ann[i].ref_id {
+                if ann[i].tig_start == ann[i - 1].tig_start + ann[i - 1].match_len + 1
+                    && ann[i].ref_start == ann[i - 1].ref_start + ann[i - 1].match_len
                 {
                     shift = true;
                 }
-                if ann[i].f0 == ann[i - 1].f0 + ann[i - 1].f1
-                    && ann[i].f3 == ann[i - 1].f3 + ann[i - 1].f1 + 1
+                if ann[i].tig_start == ann[i - 1].tig_start + ann[i - 1].match_len
+                    && ann[i].ref_start == ann[i - 1].ref_start + ann[i - 1].match_len + 1
                 {
                     shift = true;
                 }
@@ -102,7 +102,7 @@ fn main() {
         }
         let mut match_len = 0;
         for j in 0..ann.len() {
-            match_len += ann[j].f1;
+            match_len += ann[j].match_len;
         }
         let mut log0 = Vec::<u8>::new();
         print_cdr3_using_ann(&seq, &refdata, &ann, &mut log0);