Patch module name from oa2 to obitools

2025-12-08 08:40:26 +00:00 · 2022-01-13 23:43:01 +01:00
parent f53bf1b804
commit b9b9c0f179
47 changed files with 82 additions and 401 deletions
--- a/pkg/obialign/alignment.go
+++ b/pkg/obialign/alignment.go
@@ -3,7 +3,7 @@ package obialign
 import (
 	"math"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 type __build_align_arena__ struct {
--- a/pkg/obialign/fourbitsencode.go
+++ b/pkg/obialign/fourbitsencode.go
@@ -1,7 +1,7 @@
 package obialign

 import (
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 var __four_bits_base_code__ = []byte{0b0000,
--- a/pkg/obialign/pairedendalign.go
+++ b/pkg/obialign/pairedendalign.go
@@ -3,8 +3,8 @@ package obialign
 import (
 	"log"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obikmer"
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 type __pe_align_arena__ struct {
--- a/pkg/obiapat/pattern.go
+++ b/pkg/obiapat/pattern.go
@@ -10,7 +10,7 @@ import (
 	"errors"
 	"unsafe"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 var MAX_PAT_LEN = int(C.MAX_PAT_LEN)
--- a/pkg/obiapat/pcr.go
+++ b/pkg/obiapat/pcr.go
@@ -1,8 +1,8 @@
 package obiapat

 import (
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/goutils"
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 type __options__ struct {
--- a/pkg/obiformats/ecopcr_read.go
+++ b/pkg/obiformats/ecopcr_read.go
@@ -10,7 +10,7 @@ import (
 	"strconv"
 	"strings"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 type __ecopcr_file__ struct {
--- a/pkg/obiformats/embl_read.go
+++ b/pkg/obiformats/embl_read.go
@@ -11,7 +11,7 @@ import (
 	"strings"
 	"time"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 var __FILE_CHUNK_SIZE__ = 1 << 20
--- a/pkg/obiformats/fastseq_header.go
+++ b/pkg/obiformats/fastseq_header.go
@@ -3,7 +3,7 @@ package obiformats
 import (
 	"strings"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 func ParseGuessedFastSeqHeader(sequence obiseq.BioSequence) {
--- a/pkg/obiformats/fastseq_interface.go
+++ b/pkg/obiformats/fastseq_interface.go
@@ -1,5 +1,5 @@
 package obiformats

-import "git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"

 type FormatHeader func(sequence obiseq.BioSequence) string
--- a/pkg/obiformats/fastseq_json_header.go
+++ b/pkg/obiformats/fastseq_json_header.go
@@ -3,7 +3,7 @@ package obiformats
 import (
 	"strings"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	"github.com/goccy/go-json"
 )

--- a/pkg/obiformats/fastseq_obi_header.go
+++ b/pkg/obiformats/fastseq_obi_header.go
@@ -7,7 +7,7 @@ import (
 	"strconv"
 	"strings"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	"github.com/goccy/go-json"
 )

--- a/pkg/obiformats/fastseq_read.go
+++ b/pkg/obiformats/fastseq_read.go
@@ -14,8 +14,8 @@ import (
 	"time"
 	"unsafe"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/cutils"
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/cutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 func __fastseq_reader__(seqfile C.fast_kseq_p,
--- a/pkg/obiformats/fastseq_write_fasta.go
+++ b/pkg/obiformats/fastseq_write_fasta.go
@@ -10,7 +10,7 @@ import (
 	"sync"
 	"time"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 func min(x, y int) int {
--- a/pkg/obiformats/fastseq_write_fastq.go
+++ b/pkg/obiformats/fastseq_write_fastq.go
@@ -8,7 +8,7 @@ import (
 	"os"
 	"time"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 func FormatFastq(seq obiseq.BioSequence, quality_shift int, formater FormatHeader) string {
--- a/pkg/obiformats/ncbitaxdump/read.go
+++ b/pkg/obiformats/ncbitaxdump/read.go
@@ -12,7 +12,7 @@ import (
 	"strconv"
 	"strings"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitax"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
 )

 func loadNodeTable(reader io.Reader, taxonomy *obitax.Taxonomy) {
--- a/pkg/obiformats/options.go
+++ b/pkg/obiformats/options.go
@@ -1,6 +1,6 @@
 package obiformats

-import "git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"

 type __options__ struct {
 	fastseq_header_parser obiseq.SeqAnnotator
--- a/pkg/obiformats/universal_read.go
+++ b/pkg/obiformats/universal_read.go
@@ -8,7 +8,7 @@ import (
 	"os"
 	"strings"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 func GuessSeqFileType(firstline string) string {
--- a/pkg/obiformats/universal_write.go
+++ b/pkg/obiformats/universal_write.go
@@ -6,7 +6,7 @@ import (
 	"log"
 	"os"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 func WriteSequences(iterator obiseq.IBioSequence,
--- a/pkg/obikmer/encodefourmer.go
+++ b/pkg/obikmer/encodefourmer.go
@@ -1,6 +1,6 @@
 package obikmer

-import "git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"

 var __single_base_code__ = []byte{0,
 	//     A,  B,  C,  D,
--- a/pkg/obiseq/biosequence.go
+++ b/pkg/obiseq/biosequence.go
@@ -4,7 +4,7 @@ import (
 	"bytes"
 	"crypto/md5"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 )

 type Quality []uint8
--- a/pkg/obiseq/join.go
+++ b/pkg/obiseq/join.go
@@ -1,6 +1,6 @@
 package obiseq

-import "git.metabarcoding.org/lecasofts/go/oa2/pkg/goutils"
+import "git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"

 func (sequence BioSequence) Join(seq2 BioSequence, copy_annot bool) (BioSequence, error) {

--- a/pkg/obiseq/subseq.go
+++ b/pkg/obiseq/subseq.go
@@ -4,7 +4,7 @@ import (
 	"errors"
 	"fmt"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 )

 // Returns a sub sequence start from position 'from' included,
--- a/pkg/obitools/obiconvert/sequence_reader.go
+++ b/pkg/obitools/obiconvert/sequence_reader.go
@@ -6,8 +6,8 @@ import (
 	"path/filepath"
 	"strings"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiformats"
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 func __expand_list_of_files__(check_ext bool, filenames ...string) ([]string, error) {
--- a/pkg/obitools/obiconvert/sequence_writer.go
+++ b/pkg/obitools/obiconvert/sequence_writer.go
@@ -3,8 +3,8 @@ package obiconvert
 import (
 	"log"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiformats"
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 func WriteBioSequences(iterator obiseq.IBioSequence, filenames ...string) error {
--- a/pkg/obitools/obifind/iterator.go
+++ b/pkg/obitools/obifind/iterator.go
@@ -4,7 +4,7 @@ import (
 	"bytes"
 	"fmt"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitax"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
 )

 func IFilterRankRestriction() func(*obitax.ITaxonSet) *obitax.ITaxonSet {
--- a/pkg/obitools/obifind/options.go
+++ b/pkg/obitools/obifind/options.go
@@ -3,8 +3,8 @@ package obifind
 import (
 	"errors"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiformats/ncbitaxdump"
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitax"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats/ncbitaxdump"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
 	"github.com/DavidGamba/go-getoptions"
 )

--- a/pkg/obitools/obipairing/options.go
+++ b/pkg/obitools/obipairing/options.go
@@ -1,8 +1,8 @@
 package obipairing

 import (
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
 	"github.com/DavidGamba/go-getoptions"
 )

--- a/pkg/obitools/obipairing/pairing.go
+++ b/pkg/obitools/obipairing/pairing.go
@@ -6,8 +6,8 @@ import (
 	"os"
 	"time"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obialign"
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	"github.com/schollz/progressbar/v3"
 )

--- a/pkg/obitools/obipcr/options.go
+++ b/pkg/obitools/obipcr/options.go
@@ -3,8 +3,8 @@ package obipcr
 import (
 	"log"

-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiapat"
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
 	"github.com/DavidGamba/go-getoptions"
 )

--- a/pkg/obitools/obipcr/pcr.go
+++ b/pkg/obitools/obipcr/pcr.go
@@ -1,8 +1,8 @@
 package obipcr

 import (
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiapat"
-	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

 func PCR(iterator obiseq.IBioSequenceBatch) (obiseq.IBioSequence, error) {