From 38dcd98d4a339010c82702e516ced20b0ec511b1 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Tue, 17 Jun 2025 08:52:45 +0200
Subject: [PATCH] Patch the genbank parser automata

---
 ecoprimers                     |  1 +
 pkg/obiformats/genbank_read.go | 16 ++++++++--------
 pkg/obioptions/version.go      |  2 +-
 3 files changed, 10 insertions(+), 9 deletions(-)
 create mode 160000 ecoprimers

diff --git a/ecoprimers b/ecoprimers
new file mode 160000
index 0000000..b755220
--- /dev/null
+++ b/ecoprimers
@@ -0,0 +1 @@
+Subproject commit b7552200bd876851f0655a0573bcb49388811e2e
diff --git a/pkg/obiformats/genbank_read.go b/pkg/obiformats/genbank_read.go
index 4d57235..6c23ef6 100644
--- a/pkg/obiformats/genbank_read.go
+++ b/pkg/obiformats/genbank_read.go
@@ -56,7 +56,7 @@ func GenbankChunkParser(withFeatureTable bool) func(string, io.Reader) (obiseq.B
 
 				case strings.HasPrefix(line, "LOCUS       "):
 					if state != inHeader {
-						log.Fatalf("Unexpected state %d while reading LOCUS: %s", state, line)
+						log.Fatalf("Line %d - Unexpected state %d while reading LOCUS: %s", nl, state, line)
 					}
 					id = strings.SplitN(line[12:], " ", 2)[0]
 					match_length := _seqlenght_rx.FindStringSubmatch(line)
@@ -76,7 +76,7 @@ func GenbankChunkParser(withFeatureTable bool) func(string, io.Reader) (obiseq.B
 
 				case strings.HasPrefix(line, "DEFINITION  "):
 					if state != inEntry {
-						log.Fatalf("Unexpected state %d while reading DEFINITION: %s", state, line)
+						log.Fatalf("Line %d - Unexpected state %d while reading DEFINITION: %s", nl, state, line)
 					}
 					defBytes.WriteString(strings.TrimSpace(line[12:]))
 					state = inDefinition
@@ -93,29 +93,29 @@ func GenbankChunkParser(withFeatureTable bool) func(string, io.Reader) (obiseq.B
 
 				case strings.HasPrefix(line, "SOURCE      "):
 					if state != inEntry {
-						log.Fatalf("Unexpected state %d while reading SOURCE: %s", state, line)
+						log.Fatalf("Line %d - Unexpected state %d while reading SOURCE: %s", nl, state, line)
 					}
 					scientificName = strings.TrimSpace(line[12:])
 					processed = true
 
 				case strings.HasPrefix(line, "FEATURES    "):
 					if state != inEntry {
-						log.Fatalf("Unexpected state %d while reading FEATURES: %s", state, line)
+						log.Fatalf("Line %d - Unexpected state %d while reading FEATURES: %s", nl, state, line)
 					}
 					featBytes.WriteString(line)
 					state = inFeature
 					processed = true
 
 				case strings.HasPrefix(line, "ORIGIN"):
-					if state != inFeature {
-						log.Fatalf("Unexpected state %d while reading ORIGIN: %s", state, line)
+					if state != inFeature && state != inContig {
+						log.Fatalf("Line %d - Unexpected state %d while reading ORIGIN: %s", nl, state, line)
 					}
 					state = inSequence
 					processed = true
 
 				case strings.HasPrefix(line, "CONTIG"):
 					if state != inFeature && state != inContig {
-						log.Fatalf("Unexpected state %d while reading ORIGIN: %s", state, line)
+						log.Fatalf("Line %d - Unexpected state %d while reading ORIGIN: %s", nl, state, line)
 					}
 					state = inContig
 					processed = true
@@ -123,7 +123,7 @@ func GenbankChunkParser(withFeatureTable bool) func(string, io.Reader) (obiseq.B
 				case line == "//":
 
 					if state != inSequence && state != inContig {
-						log.Fatalf("Unexpected state %d while reading end of record %s", state, id)
+						log.Fatalf("Line %d - Unexpected state %d while reading end of record %s", nl, state, id)
 					}
 					// log.Debugln("Total lines := ", nl)
 					if id == "" {
diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go
index fa7137f..20de387 100644
--- a/pkg/obioptions/version.go
+++ b/pkg/obioptions/version.go
@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "d31e677"
+var _Commit = "7b23985"
 var _Version = "Release 4.4.0"
 
 // Version returns the version of the obitools package.