Improve tests

bio/slow5/example_test.go

@@ -31,3 +31,34 @@ func ExampleNewParser() {
 	fmt.Println(outputReads[0].RawSignal[0:10])
 	// Output: [430 472 463 467 454 465 463 450 450 449]
 }
+
+func ExampleSvbCompressRawSignal() {
+	// example.slow5 is a file I generated using slow5tools from nanopore fast5
+	// run where I was testing using nanopore for doing COVID testing. It
+	// contains real nanopore data.
+	file, _ := os.Open("data/example.slow5")
+	defer file.Close()
+	// Set maxLineSize to 64kb. If you expect longer reads,
+	// make maxLineSize longer!
+	const maxLineSize = 2 * 32 * 1024
+	parser, _ := slow5.NewParser(file, maxLineSize)
+	read, _ := parser.Next()
+
+	// Get the raw signal from a read
+	rawSignal := read.RawSignal
+
+	// Compress that raw signal into a mask and data
+	mask, data := slow5.SvbCompressRawSignal(rawSignal)
+
+	// Decompress mask and data back into raw signal
+	rawSignalDecompressed := slow5.SvbDecompressRawSignal(len(rawSignal), mask, data)
+
+	for idx := range rawSignal {
+		if rawSignal[idx] != rawSignalDecompressed[idx] {
+			fmt.Println("Compression failed!")
+		}
+	}
+	fmt.Println(data[:10])
+
+	// Output: [174 1 216 1 207 1 211 1 198 1]
+}

bio/slow5/slow5_test.go

@@ -225,3 +225,32 @@ func TestSimpleExample(t *testing.T) {
 	}
 
 }
+
+func TestSvb(t *testing.T) {
+	file, _ := os.Open("data/example.slow5")
+	defer file.Close()
+	const maxLineSize = 2 * 32 * 1024
+	parser, _ := NewParser(file, maxLineSize)
+	var outputReads []Read
+	for {
+		read, err := parser.Next()
+		if err != nil {
+			if !errors.Is(err, io.EOF) {
+				t.Errorf("Got unknown error: %s", err)
+			}
+			break
+		}
+		outputReads = append(outputReads, *read)
+	}
+
+	for readNum, read := range outputReads {
+		rawSignal := read.RawSignal
+		mask, data := SvbCompressRawSignal(rawSignal)
+		rawSignalDecompressed := SvbDecompressRawSignal(len(rawSignal), mask, data)
+		for idx := range rawSignal {
+			if rawSignal[idx] != rawSignalDecompressed[idx] {
+				t.Errorf("Read signal at readNum %d idx %d didn't match decompressed signal %d", readNum, rawSignal[idx], rawSignalDecompressed[idx])
+			}
+		}
+	}
+}

go.mod

@@ -15,6 +15,8 @@ require (
 
 require (
 	github.com/davecgh/go-spew v1.1.1 // indirect
+	github.com/intel-go/cpuid v0.0.0-20181003105527-1a4a6f06a1c6 // indirect
+	github.com/koeng101/svb v0.0.0-20230815034912-d6737f9ed8b8 // indirect
 	github.com/mattn/go-sqlite3 v1.14.13 // indirect
 	golang.org/x/sync v0.3.0 // indirect
 )

go.sum

@@ -3,8 +3,12 @@ github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/google/go-cmp v0.5.8 h1:e6P7q2lk1O+qJJb4BtCQXlK8vWEO8V1ZeuEdJNOqZyg=
 github.com/google/go-cmp v0.5.8/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY=
+github.com/intel-go/cpuid v0.0.0-20181003105527-1a4a6f06a1c6 h1:XboatR7lasl05yel5hNXF7kQBw2oFUGdMztcgisfhNU=
+github.com/intel-go/cpuid v0.0.0-20181003105527-1a4a6f06a1c6/go.mod h1:RmeVYf9XrPRbRc3XIx0gLYA8qOFvNoPOfaEZduRlEp4=
 github.com/klauspost/cpuid v1.3.1 h1:5JNjFYYQrZeKRJ0734q51WCEEn2huer72Dc7K+R/b6s=
 github.com/klauspost/cpuid v1.3.1/go.mod h1:bYW4mA6ZgKPob1/Dlai2LviZJO7KGI3uoWLd42rAQw4=
+github.com/koeng101/svb v0.0.0-20230815034912-d6737f9ed8b8 h1:oaPrvMY8VJEYfJ/r/VTKh2zshX/SxYHcImJRPZ++JPI=
+github.com/koeng101/svb v0.0.0-20230815034912-d6737f9ed8b8/go.mod h1:/zIPMIRhcEjka8JxY3mo7jexMl4ncHLRUnv9RIiAS9E=
 github.com/kr/pretty v0.1.0 h1:L/CwN0zerZDmRFUapSPitk6f+Q3+0za1rQkzVuMiMFI=
 github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo=
 github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ=
@@ -16,6 +20,7 @@ github.com/mattn/go-sqlite3 v1.14.13 h1:1tj15ngiFfcZzii7yd82foL+ks+ouQcj8j/TPq3f
 github.com/mattn/go-sqlite3 v1.14.13/go.mod h1:NyWgC/yNuGj7Q9rpYnZvas74GogHl5/Z4A/KQRfk6bU=
 github.com/mitchellh/go-wordwrap v1.0.1 h1:TLuKupo69TCn6TQSyGxwI1EblZZEsQ0vMlAFQflz0v0=
 github.com/mitchellh/go-wordwrap v1.0.1/go.mod h1:R62XHJLzvMFRBbcrT7m7WgmE1eOyTSsCt+hzestvNj0=
+github.com/mmcloughlin/avo v0.0.0-20200504053806-fa88270b07e4/go.mod h1:wqKykBG2QzQDJEzvRkcS8x6MiSJkF52hXZsXcjaB3ls=
 github.com/mroth/weightedrand v0.4.1 h1:rHcbUBopmi/3x4nnrvwGJBhX9d0vk+KgoLUZeDP6YyI=
 github.com/mroth/weightedrand v0.4.1/go.mod h1:3p2SIcC8al1YMzGhAIoXD+r9olo/g/cdJgAD905gyNE=
 github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
@@ -25,10 +30,28 @@ github.com/sergi/go-diff v1.2.0/go.mod h1:STckp+ISIX8hZLjrqAeVduY0gWCT9IjLuqbuNX
 github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
 github.com/stretchr/testify v1.4.0 h1:2E4SXV/wtOkTonXsotYi4li6zVWxYlZuYNCXe9XRJyk=
 github.com/stretchr/testify v1.4.0/go.mod h1:j7eGeouHqKxXV5pUuKE4zz7dFj8WfuZ+81PSLYec5m4=
+github.com/yuin/goldmark v1.1.27/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74=
+golang.org/x/arch v0.0.0-20190909030613-46d78d1859ac/go.mod h1:flIaEI6LNU6xOCD5PaJvn9wGP0agmIOqjrtsKGRguv4=
+golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
+golang.org/x/crypto v0.0.0-20191011191535-87dc89f01550/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI=
 golang.org/x/exp v0.0.0-20230310171629-522b1b587ee0 h1:LGJsf5LRplCck6jUCH3dBL2dmycNruWNF5xugkSlfXw=
 golang.org/x/exp v0.0.0-20230310171629-522b1b587ee0/go.mod h1:CxIveKay+FTh1D0yPZemJVgC/95VzuuOLq5Qi4xnoYc=
+golang.org/x/mod v0.2.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
+golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
+golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
+golang.org/x/net v0.0.0-20200226121028-0de0cce0169b/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
+golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
+golang.org/x/sync v0.0.0-20190911185100-cd5d95a43a6e/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
 golang.org/x/sync v0.3.0 h1:ftCYgMx6zT/asHUrPw8BLLscYtGznsLAnjq5RH9P66E=
 golang.org/x/sync v0.3.0/go.mod h1:FU7BRWz2tNW+3quACPkgCx/L+uEAv1htQ0V83Z9Rj+Y=
+golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
+golang.org/x/sys v0.0.0-20190412213103-97732733099d/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
+golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
+golang.org/x/tools v0.0.0-20200425043458-8463f397d07c/go.mod h1:EkVYQZoAsY45+roYkvgYkIh4xh/qjgUK9TdY2XT94GE=
+golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
+golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
+golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 h1:YR8cESwS4TdDjEe65xsg0ogRM/Nc3DYOhEAlW+xobZo=
 gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
@@ -38,3 +61,4 @@ gopkg.in/yaml.v2 v2.4.0 h1:D8xgwECY7CYvx+Y2n4sBz93Jn9JRvxdiyyo8CTfuKaY=
 gopkg.in/yaml.v2 v2.4.0/go.mod h1:RDklbk79AGWmwhnvt/jBztapEOGDOx6ZbXqjP6csGnQ=
 lukechampine.com/blake3 v1.1.5 h1:hsACfxWvLdGmjYbWGrumQIphOvO+ZruZehWtgd2fxoM=
 lukechampine.com/blake3 v1.1.5/go.mod h1:hE8RpzdO8ttZ7446CXEwDP1eu2V4z7stv0Urj1El20g=
+rsc.io/pdf v0.1.1/go.mod h1:n8OzWcQ6Sp37PL01nO98y4iUCRdTGarVfzxY20ICaU4=