From dd22815f138c46849a9a7f4c0142eaf499b8c6ec Mon Sep 17 00:00:00 2001
From: ygidtu <ygidtu@gmail.com>
Date: Fri, 17 Jul 2020 09:56:29 +0800
Subject: [PATCH] fix bugs while processing with cigar

---
 build.sh |  1 +
 const.go |  2 +-
 fast.go  | 13 ++++++++++++-
 slow.go  |  5 ++++-
 4 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/build.sh b/build.sh
index 50be217..8a03abe 100644
--- a/build.sh
+++ b/build.sh
@@ -4,3 +4,4 @@ env GOOS=darwin GOARCH=amd64 go build -o REDItools2_darwin_amd64 .
 env GOOS=linux GOARCH=amd64 go build -o REDItools2_linux_amd64 .
 env GOOS=windows GOARCH=amd64 go build -o REDItools2_win_amd64.exe .
 
+# scp -P 1100 REDItools2_linux_amd64 zhangyiming@chenlinlab.synology.me:/mnt/data8/zhangyiming/REDItools2
diff --git a/const.go b/const.go
index fa7c0d0..2465d03 100644
--- a/const.go
+++ b/const.go
@@ -20,7 +20,7 @@ var conf config
 var region *Region
 
 const (
-	VERSION            = "0.0.3-beta"
+	VERSION            = "0.0.4-beta"
 	DefaultBaseQuality = 30
 )
 
diff --git a/fast.go b/fast.go
index eb4308e..b660c98 100644
--- a/fast.go
+++ b/fast.go
@@ -56,8 +56,10 @@ func workerFast(
 			}
 
 			start, index := 0, 0
+
 			for _, i := range record.Cigar {
 				if i.Type() == sam.CigarMatch {
+
 					for j := 1; j <= i.Len(); j++ {
 						at := index + j - 1
 
@@ -69,6 +71,11 @@ func workerFast(
 						genomic := start + record.Start
 
 						if _, ok := edits[genomic]; !ok {
+							// GL000220.1
+							if genomic - 1 >= len(chrRef) {
+								sugar.Error(record.Record)
+								sugar.Fatalf("%s: genomic - 1[%d] >= len(chrRef)[%d]", ref.Ref, genomic - 1, len(chrRef))
+							}
 							edits[genomic] = NewEditsInfo(ref.Ref, chrRef[genomic-1], genomic)
 						}
 
@@ -76,7 +83,11 @@ func workerFast(
 						start++
 					}
 					index += i.Len()
-				} else if i.Type() != sam.CigarDeletion || i.Type() != sam.CigarHardClipped || i.Type() != sam.CigarInsertion {
+				} else if i.Type() != sam.CigarDeletion &&
+					i.Type() != sam.CigarHardClipped &&
+					i.Type() != sam.CigarInsertion &&
+					i.Type() != sam.CigarSoftClipped {
+
 					start += i.Len()
 				}
 			}
diff --git a/slow.go b/slow.go
index e7449a7..b247b64 100644
--- a/slow.go
+++ b/slow.go
@@ -73,7 +73,10 @@ func worker(wg *sync.WaitGroup, refs chan *Region, w chan string, omopolymericPo
 						start++
 					}
 					index += i.Len()
-				} else if i.Type() != sam.CigarDeletion || i.Type() != sam.CigarHardClipped || i.Type() != sam.CigarInsertion {
+				} else if i.Type() != sam.CigarDeletion &&
+					i.Type() != sam.CigarHardClipped &&
+					i.Type() != sam.CigarInsertion &&
+					i.Type() != sam.CigarSoftClipped {
 					start += i.Len()
 				}
 			}