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Patch module name from oa2 to obitools

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This commit is contained in:
Eric Coissac
2022-01-13 23:43:01 +01:00
parent f53bf1b804
commit b9b9c0f179
47 changed files with 82 additions and 401 deletions
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pkg/obiformats/ecopcr_read.go
+1 -1
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@@ -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 {
pkg/obiformats/embl_read.go
+1 -1
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@@ -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
pkg/obiformats/fastseq_header.go
+1 -1
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@@ -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) {
pkg/obiformats/fastseq_interface.go
+1 -1
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@@ -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
pkg/obiformats/fastseq_json_header.go
+1 -1
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@@ -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"
)
pkg/obiformats/fastseq_obi_header.go
+1 -1
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@@ -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"
)
pkg/obiformats/fastseq_read.go
+2 -2
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@@ -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,
pkg/obiformats/fastseq_write_fasta.go
+1 -1
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@@ -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 {
pkg/obiformats/fastseq_write_fastq.go
+1 -1
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@@ -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 {
pkg/obiformats/ncbitaxdump/read.go
+1 -1
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@@ -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) {
pkg/obiformats/options.go
+1 -1
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@@ -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
pkg/obiformats/universal_read.go
+1 -1
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@@ -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 {
pkg/obiformats/universal_write.go
+1 -1
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@@ -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,