From 85153e038a64156f2c123ab689231367a75661e6 Mon Sep 17 00:00:00 2001
From: ygidtu <ygidtu@gmail.com>
Date: Sat, 18 Jul 2020 11:03:00 +0800
Subject: [PATCH] fix bugs while processing genomic locations

---
 const.go |  7 ++++---
 fast.go  | 15 +++------------
 slow.go  |  4 +---
 3 files changed, 8 insertions(+), 18 deletions(-)

diff --git a/const.go b/const.go
index d9c9961..ff1a523 100644
--- a/const.go
+++ b/const.go
@@ -1,6 +1,7 @@
 package main
 
 import (
+	"bytes"
 	"fmt"
 	"regexp"
 	"strconv"
@@ -20,7 +21,7 @@ var conf config
 var region *Region
 
 const (
-	VERSION            = "0.0.4-beta"
+	VERSION            = "0.0.5-beta"
 	DefaultBaseQuality = 30
 )
 
@@ -298,7 +299,7 @@ type EditsInfo struct {
 
 func NewEditsInfo(lastChr string, ref byte, pos int) *EditsInfo {
 	return &EditsInfo{
-		LastChr: lastChr, Ref: ref, Edits: []byte{}, Pos: pos,
+		LastChr: lastChr, Ref: bytes.ToUpper([]byte{ref})[0], Edits: []byte{}, Pos: pos,
 		Counter:  map[byte]int{'A': 0, 'T': 0, 'C': 0, 'G': 0},
 		Variants: map[byte]int{'A': 0, 'T': 0, 'C': 0, 'G': 0},
 		Strand:   "", Qualities: []byte{}, Total: 0,
@@ -311,7 +312,7 @@ func (e *EditsInfo) AddReads(record *Record, at int) {
 	if seq != 'N' {
 		e.Counter[e.Ref]++
 		e.Qualities = append(e.Qualities, record.QualityAt(at)) //
-		e.Edits = append(e.Edits, seq)
+		e.Edits = append(e.Edits, bytes.ToUpper([]byte{seq})[0])
 		e.Strand += record.Strand()
 
 		if e.Ref != seq {
diff --git a/fast.go b/fast.go
index b660c98..c72881b 100644
--- a/fast.go
+++ b/fast.go
@@ -19,15 +19,6 @@ func workerFast(
 			break
 		}
 
-		//chrRef, err := fetchFasta(ref.ToRegion())
-		//if err != nil {
-		//	sugar.Warnf("try to modify %s", ref)
-		//	chrRef, err = fetchFasta(ref.SwitchRegion())
-		//}
-		//if err != nil {
-		//	sugar.Fatal(err)
-		//}
-
 		chrRef, ok := chrRefs[ref.Ref]
 		if !ok {
 			sugar.Errorf("failed to get %s from reference", ref.Ref)
@@ -72,11 +63,11 @@ func workerFast(
 
 						if _, ok := edits[genomic]; !ok {
 							// GL000220.1
-							if genomic - 1 >= len(chrRef) {
+							if genomic >= len(chrRef) {
 								sugar.Error(record.Record)
-								sugar.Fatalf("%s: genomic - 1[%d] >= len(chrRef)[%d]", ref.Ref, genomic - 1, len(chrRef))
+								sugar.Fatalf("%s: genomic - 1[%d] >= len(chrRef)[%d]", ref.Ref, genomic, len(chrRef))
 							}
-							edits[genomic] = NewEditsInfo(ref.Ref, chrRef[genomic-1], genomic)
+							edits[genomic] = NewEditsInfo(ref.Ref, chrRef[genomic], genomic + 1)
 						}
 
 						edits[genomic].AddReads(record, at)
diff --git a/slow.go b/slow.go
index b247b64..2172df8 100644
--- a/slow.go
+++ b/slow.go
@@ -61,12 +61,10 @@ func worker(wg *sync.WaitGroup, refs chan *Region, w chan string, omopolymericPo
 							sugar.Fatal(record.SeqString())
 						}
 
-						// record.QueryPosition = append(record.QueryPosition, at)
-
 						genomic := start + record.Start
 
 						if _, ok := edits[genomic]; !ok {
-							edits[genomic] = NewEditsInfo(ref.Chrom, chrRef[genomic-1], genomic)
+							edits[genomic] = NewEditsInfo(ref.Chrom, chrRef[genomic], genomic + 1)
 						}
 
 						edits[genomic].AddReads(record, at)