Adds some unit test

Former-commit-id: b1a59df1c87187a1538f30c447d42bbe96402419

go.mod

@@ -1,6 +1,6 @@
 module git.metabarcoding.org/lecasofts/go/obitools
 
-go 1.20
+go 1.21
 
 require (
 	github.com/DavidGamba/go-getoptions v0.28.0
@@ -13,6 +13,7 @@ require (
 	github.com/rrethy/ahocorasick v1.0.0
 	github.com/schollz/progressbar/v3 v3.13.1
 	github.com/sirupsen/logrus v1.9.3
+	github.com/stretchr/testify v1.7.0
 	github.com/tevino/abool/v2 v2.1.0
 	golang.org/x/exp v0.0.0-20231006140011-7918f672742d
 	gonum.org/v1/gonum v0.14.0
@@ -20,8 +21,11 @@ require (
 )
 
 require (
+	github.com/davecgh/go-spew v1.1.1 // indirect
 	github.com/kr/pretty v0.2.1 // indirect
 	github.com/kr/text v0.1.0 // indirect
+	github.com/pmezard/go-difflib v1.0.0 // indirect
+	gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c // indirect
 )
 
 require (

go.work

@@ -0,0 +1,3 @@
+go 1.21.3
+
+use .

go.work.sum

@@ -0,0 +1,15 @@
+git.sr.ht/~sbinet/gg v0.3.1/go.mod h1:KGYtlADtqsqANL9ueOFkWymvzUvLMQllU5Ixo+8v3pc=
+github.com/ajstarks/svgo v0.0.0-20211024235047-1546f124cd8b/go.mod h1:1KcenG0jGWcpt8ov532z81sp/kMMUG485J2InIOyADM=
+github.com/go-fonts/liberation v0.3.0/go.mod h1:jdJ+cqF+F4SUL2V+qxBth8fvBpBDS7yloUL5Fi8GTGY=
+github.com/go-latex/latex v0.0.0-20230307184459-12ec69307ad9/go.mod h1:gWuR/CrFDDeVRFQwHPvsv9soJVB/iqymhuZQuJ3a9OM=
+github.com/go-pdf/fpdf v0.6.0/go.mod h1:HzcnA+A23uwogo0tp9yU+l3V+KXhiESpt1PMayhOh5M=
+github.com/goccmack/gocc v0.0.0-20230228185258-2292f9e40198/go.mod h1:DTh/Y2+NbnOVVoypCCQrovMPDKUGp4yZpSbWg5D0XIM=
+github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0/go.mod h1:E/TSTwGwJL78qG/PmXZO1EjYhfJinVAhrmmHX6Z8B9k=
+github.com/google/go-cmp v0.5.8/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY=
+golang.org/x/crypto v0.14.0/go.mod h1:MVFd36DqK4CsrnJYDkBA3VC4m2GkXAM0PvzMCn4JQf4=
+golang.org/x/image v0.6.0/go.mod h1:MXLdDR43H7cDJq5GEGXEVeeNhPgi+YYEQ2pC1byI1x0=
+golang.org/x/mod v0.13.0/go.mod h1:hTbmBsO62+eylJbnUtE2MGJUyE7QWk4xUqPFrRgJ+7c=
+golang.org/x/text v0.13.0/go.mod h1:TvPlkZtksWOMsz7fbANvkp4WM8x/WCo/om8BMLbz+aE=
+golang.org/x/tools v0.14.0/go.mod h1:uYBEerGOWcJyEORxN+Ek8+TT266gXkNlHdJBwexUsBg=
+gonum.org/v1/plot v0.10.1/go.mod h1:VZW5OlhkL1mysU9vaqNHnsy86inf6Ot+jB3r+BczCEo=
+rsc.io/pdf v0.1.1/go.mod h1:n8OzWcQ6Sp37PL01nO98y4iUCRdTGarVfzxY20ICaU4=

pkg/obiseq/subseq.go

@@ -5,8 +5,16 @@ import (
 	"fmt"
 )
 
-// Returns a sub sequence start from position 'from' included,
-// to position 'to' excluded. Coordinates start at position 0.
+// Subsequence returns a subsequence of the BioSequence.
+//
+// Parameters:
+// - from: starting position of the subsequence.
+// - to: ending position of the subsequence.
+// - circular: indicates whether the subsequence should be circular.
+//
+// Return:
+// - *BioSequence: the subsequence of the BioSequence.
+// - error: an error if the subsequence parameters are invalid.
 func (sequence *BioSequence) Subsequence(from, to int, circular bool) (*BioSequence, error) {
 	if from >= to && !circular {
 		return nil, errors.New("from greater than to")

pkg/obiseq/subseq_test.go

@@ -0,0 +1,48 @@
+package obiseq
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestSubsequence(t *testing.T) {
+	// Test case 1: Subsequence with valid parameters and non-circular
+	seq := NewBioSequence("ID1", []byte("ATCG"), "")
+	sub, err := seq.Subsequence(1, 3, false)
+	assert.NoError(t, err)
+	assert.Equal(t, []byte("tc"), sub.Sequence())
+
+	seq = NewBioSequenceWithQualities("ID1", []byte("ATCG"), "", []byte{40, 30, 20, 10})
+	sub, err = seq.Subsequence(1, 3, false)
+	assert.NoError(t, err)
+	assert.Equal(t, []byte("tc"), sub.Sequence())
+	assert.Equal(t, Quality([]byte{30, 20}), sub.Qualities())
+
+	// Test case 2: Subsequence with valid parameters and circular
+	seq2 := NewBioSequence("ID1", []byte("ATCG"), "")
+	sub2, err2 := seq2.Subsequence(3, 2, true)
+	assert.NoError(t, err2)
+	assert.Equal(t, []byte("gat"), sub2.Sequence())
+
+	seq = NewBioSequenceWithQualities("ID1", []byte("ATCG"), "", []byte{40, 30, 20, 10})
+	sub, err = seq.Subsequence(3, 2, true)
+	assert.NoError(t, err)
+	assert.Equal(t, []byte("gat"), sub.Sequence())
+	assert.Equal(t, Quality([]byte{10, 40, 30}), sub.Qualities())
+
+	// Test case 3: Subsequence with from greater than to and non-circular
+	seq3 := NewBioSequence("ID1", []byte("ATCG"), "")
+	_, err3 := seq3.Subsequence(3, 1, false)
+	assert.EqualError(t, err3, "from greater than to")
+
+	// Test case 4: Subsequence with from out of bounds
+	seq4 := NewBioSequence("ID1", []byte("ATCG"), "")
+	_, err4 := seq4.Subsequence(-1, 2, false)
+	assert.EqualError(t, err4, "from out of bounds")
+
+	// Test case 5: Subsequence with to out of bounds
+	seq5 := NewBioSequence("ID1", []byte("ATCG"), "")
+	_, err5 := seq5.Subsequence(2, 5, false)
+	assert.EqualError(t, err5, "to out of bounds")
+}