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moved align, bwt, and mash into new search package. #438

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merged 2 commits into from
Jan 18, 2024
Merged

moved align, bwt, and mash into new search package. #438

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48ca768
moved align, bwt, and mash into new search package.
TimothyStiles Jan 18, 2024
241bbdc
updated import paths.
TimothyStiles Jan 18, 2024
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2 changes: 1 addition & 1 deletion align/align.go → search/align/align.go
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Expand Up @@ -66,7 +66,7 @@ Tim
package align

import (
"github.com/bebop/poly/align/matrix"
"github.com/bebop/poly/search/align/matrix"
)

// Scoring is a struct that holds the scoring matrix for match, mismatch, and gap penalties.
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4 changes: 2 additions & 2 deletions align/align_test.go → search/align/align_test.go
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Expand Up @@ -3,9 +3,9 @@ package align_test
import (
"testing"

"github.com/bebop/poly/align"
"github.com/bebop/poly/align/matrix"
"github.com/bebop/poly/alphabet"
"github.com/bebop/poly/search/align"
"github.com/bebop/poly/search/align/matrix"
)

func TestNeedlemanWunsch(t *testing.T) {
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4 changes: 2 additions & 2 deletions align/example_test.go → search/align/example_test.go
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Expand Up @@ -4,9 +4,9 @@ package align_test
import (
"fmt"

"github.com/bebop/poly/align"
"github.com/bebop/poly/align/matrix"
"github.com/bebop/poly/alphabet"
"github.com/bebop/poly/search/align"
"github.com/bebop/poly/search/align/matrix"
)

func ExampleNeedlemanWunsch() {
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0 align/matrix/matrices.go → search/align/matrix/matrices.go
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0 align/matrix/matrix.go → search/align/matrix/matrix.go
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2 changes: 1 addition & 1 deletion align/matrix/matrix_test.go → search/align/matrix/matrix_test.go
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Expand Up @@ -3,8 +3,8 @@ package matrix_test
import (
"testing"

"github.com/bebop/poly/align/matrix"
"github.com/bebop/poly/alphabet"
"github.com/bebop/poly/search/align/matrix"
"github.com/stretchr/testify/assert"
)

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0 bwt/bitvector.go → search/bwt/bitvector.go
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0 bwt/bitvector_test.go → search/bwt/bitvector_test.go
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0 bwt/bwt.go → search/bwt/bwt.go
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0 bwt/bwt_test.go → search/bwt/bwt_test.go
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2 changes: 1 addition & 1 deletion bwt/example_test.go → search/bwt/example_test.go
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Expand Up @@ -4,7 +4,7 @@ import (
"fmt"
"log"

"github.com/bebop/poly/bwt"
"github.com/bebop/poly/search/bwt"
"golang.org/x/exp/slices"
)

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0 bwt/rsa_bitvector.go → search/bwt/rsa_bitvector.go
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0 bwt/rsa_bitvector_test.go → search/bwt/rsa_bitvector_test.go
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0 bwt/wavelet.go → search/bwt/wavelet.go
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0 bwt/wavelet_test.go → search/bwt/wavelet_test.go
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2 changes: 1 addition & 1 deletion mash/example_test.go → search/mash/example_test.go
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Expand Up @@ -3,7 +3,7 @@ package mash_test
import (
"fmt"

"github.com/bebop/poly/mash"
"github.com/bebop/poly/search/mash"
)

func ExampleMash() {
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0 mash/mash.go → search/mash/mash.go
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2 changes: 1 addition & 1 deletion mash/mash_test.go → search/mash/mash_test.go
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Expand Up @@ -3,7 +3,7 @@ package mash_test
import (
"testing"

"github.com/bebop/poly/mash"
"github.com/bebop/poly/search/mash"
)

func TestMash(t *testing.T) {
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