From 3f579353282e14af6bf83ce299d1ad0f8a04cb86 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Mon, 5 Aug 2024 11:32:37 +0200
Subject: [PATCH] Adjust the size of the genbank and embl buffer size

---
 pkg/obiformats/embl_read.go          | 2 +-
 pkg/obiformats/genbank_read.go       | 2 +-
 pkg/obiformats/seqfile_chunk_read.go | 8 +++-----
 pkg/obioptions/version.go            | 2 +-
 4 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/pkg/obiformats/embl_read.go b/pkg/obiformats/embl_read.go
index 1cd5b3c..876866f 100644
--- a/pkg/obiformats/embl_read.go
+++ b/pkg/obiformats/embl_read.go
@@ -187,7 +187,7 @@ func _ParseEmblFile(
 func ReadEMBL(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, error) {
 	opt := MakeOptions(options)
 
-	buff := make([]byte, 1024*1024*512)
+	buff := make([]byte, 1024*1024*128) // 128 MB
 
 	entry_channel := ReadSeqFileChunk(
 		opt.Source(),
diff --git a/pkg/obiformats/genbank_read.go b/pkg/obiformats/genbank_read.go
index d6dec7e..f9dfed2 100644
--- a/pkg/obiformats/genbank_read.go
+++ b/pkg/obiformats/genbank_read.go
@@ -223,7 +223,7 @@ func ReadGenbank(reader io.Reader, options ...WithOption) (obiiter.IBioSequence,
 	opt := MakeOptions(options)
 	// entry_channel := make(chan _FileChunk)
 
-	buff := make([]byte, 1024*1024*512)
+	buff := make([]byte, 1024*1024*128) // 128 MB
 
 	entry_channel := ReadSeqFileChunk(
 		opt.Source(),
diff --git a/pkg/obiformats/seqfile_chunk_read.go b/pkg/obiformats/seqfile_chunk_read.go
index ed214ce..727325f 100644
--- a/pkg/obiformats/seqfile_chunk_read.go
+++ b/pkg/obiformats/seqfile_chunk_read.go
@@ -9,8 +9,6 @@ import (
 	log "github.com/sirupsen/logrus"
 )
 
-var _FileChunkSize = 1024 * 1024 * 10
-
 type SeqFileChunkParser func(string, io.Reader) (obiseq.BioSequenceSlice, error)
 
 type SeqFileChunk struct {
@@ -46,7 +44,7 @@ func ReadSeqFileChunk(
 
 	chunk_channel := make(ChannelSeqFileChunk)
 
-	_FileChunkSize := len(buff)
+	fileChunkSize := len(buff)
 
 	go func() {
 		size := 0
@@ -73,9 +71,9 @@ func ReadSeqFileChunk(
 			// Read from the reader in 1 MB increments until the end of the last entry is found
 			for end = splitter(buff); err == nil && end < 0; end = splitter(buff) {
 				ic++
-				buff = slices.Grow(buff, _FileChunkSize)
+				buff = slices.Grow(buff, fileChunkSize)
 				l := len(buff)
-				extbuff := buff[l:(l + _FileChunkSize - 1)]
+				extbuff := buff[l:(l + fileChunkSize - 1)]
 				size, err = io.ReadFull(reader, extbuff)
 				buff = buff[0:(l + size)]
 			}
diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go
index c208bca..a9b1642 100644
--- a/pkg/obioptions/version.go
+++ b/pkg/obioptions/version.go
@@ -7,7 +7,7 @@ import (
 // TODO: The version number is extracted from git. This induces that the version
 // corresponds to the last commit, and not the one when the file will be
 // commited
-var _Commit = "f83032e"
+var _Commit = "886b5d9"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.