How to use Read method of overlap Package

Best Mock code snippet using overlap.Read

overlap_test.go

Source:overlap_test.go Github

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...12// outside // | | S E 0/1 0/113// overlap // | S | E <1 <114// contain // S | | E 1/1 <115var _ = Describe("segment", func() {16 Context("overlapRead", func() {17 Context("match", func() {18 It("returns correct values", func() {19 Expect(overlapRead(20 testing.SimpleTime(0), testing.SimpleTime(100), // t1 t221 testing.SimpleTime(0), testing.SimpleTime(100), // st et22 10*time.Second,23 ).String()).To(Equal(big.NewRat(1, 1).String()))24 })25 })26 Context("inside", func() {27 It("returns correct values", func() {28 Expect(overlapRead(29 testing.SimpleTime(0), testing.SimpleTime(100), // t1 t230 testing.SimpleTime(10), testing.SimpleTime(90), // st et31 10*time.Second,32 ).String()).To(Equal(big.NewRat(8, 10).String()))33 Expect(overlapRead(34 testing.SimpleTime(0), testing.SimpleTime(100), // t1 t235 testing.SimpleTime(0), testing.SimpleTime(90), // st et36 10*time.Second,37 ).String()).To(Equal(big.NewRat(9, 10).String()))38 Expect(overlapRead(39 testing.SimpleTime(0), testing.SimpleTime(100), // t1 t240 testing.SimpleTime(10), testing.SimpleTime(100), // st et41 10*time.Second,42 ).String()).To(Equal(big.NewRat(9, 10).String()))43 })44 })45 Context("contain", func() {46 It("returns correct values", func() {47 Expect(overlapRead(48 testing.SimpleTime(100), testing.SimpleTime(200), // t1 t249 testing.SimpleTime(90), testing.SimpleTime(210), // st et50 10*time.Second,51 ).String()).To(Equal(big.NewRat(1, 1).String()))52 Expect(overlapRead(53 testing.SimpleTime(100), testing.SimpleTime(200), // t1 t254 testing.SimpleTime(100), testing.SimpleTime(210), // st et55 10*time.Second,56 ).String()).To(Equal(big.NewRat(1, 1).String()))57 Expect(overlapRead(58 testing.SimpleTime(100), testing.SimpleTime(200), // t1 t259 testing.SimpleTime(90), testing.SimpleTime(200), // st et60 10*time.Second,61 ).String()).To(Equal(big.NewRat(1, 1).String()))62 })63 })64 Context("overlap", func() {65 It("returns correct values", func() {66 Expect(overlapRead(67 testing.SimpleTime(100), testing.SimpleTime(200), // t1 t268 testing.SimpleTime(90), testing.SimpleTime(110), // st et69 10*time.Second,70 ).String()).To(Equal(big.NewRat(1, 10).String()))71 Expect(overlapRead(72 testing.SimpleTime(100), testing.SimpleTime(200), // t1 t273 testing.SimpleTime(190), testing.SimpleTime(210), // st et74 10*time.Second,75 ).String()).To(Equal(big.NewRat(1, 10).String()))76 })77 })78 Context("outside", func() {79 It("returns correct values", func() {80 Expect(overlapRead(81 testing.SimpleTime(100), testing.SimpleTime(200), // t1 t282 testing.SimpleTime(90), testing.SimpleTime(100), // st et83 10*time.Second,84 ).String()).To(Equal(big.NewRat(0, 1).String()))85 Expect(overlapRead(86 testing.SimpleTime(100), testing.SimpleTime(200), // t1 t287 testing.SimpleTime(80), testing.SimpleTime(90), // st et88 10*time.Second,89 ).String()).To(Equal(big.NewRat(0, 1).String()))90 Expect(overlapRead(91 testing.SimpleTime(100), testing.SimpleTime(200), // t1 t292 testing.SimpleTime(200), testing.SimpleTime(210), // st et93 10*time.Second,94 ).String()).To(Equal(big.NewRat(0, 1).String()))95 Expect(overlapRead(96 testing.SimpleTime(100), testing.SimpleTime(200), // t1 t297 testing.SimpleTime(210), testing.SimpleTime(220), // st et98 10*time.Second,99 ).String()).To(Equal(big.NewRat(0, 1).String()))100 })101 })102 })103 Context("overlapWrite", func() {104 Context("match", func() {105 It("returns correct values", func() {106 Expect(overlapWrite(107 testing.SimpleTime(0), testing.SimpleTime(100), // t1 t2108 testing.SimpleTime(0), testing.SimpleTime(100), // st et109 10*time.Second,...

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window.go

Source:window.go Github

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...19}20func (b *windowBuffer) get(offset uint) *bytes.Buffer {21 return b.items[offset%b.length]22}23func skip(reader streamconv.ItemReader, count uint) (err error) {24 for count > 0 {25 var skipped io.Reader26 skipped, err = reader.ReadItem()27 if err != nil {28 return29 }30 _, err = io.Copy(ioutil.Discard, skipped)31 if err != nil {32 return33 }34 count--35 }36 return37}38type windowReader interface {39 streamconv.ItemReader40 Initialize(first bool) (err error)41 Finalize() (err error)42}43type partialWindowReader struct {44 reader streamconv.LookaheadItemReader45 size uint46 step uint47 overlap uint48 hole uint49 bufferStep uint50 buffer *windowBuffer51 bufferIndex uint52 reusedCount uint53 readCount uint54 bufferedCount uint55 err error56}57func newPartialWindowReader(reader streamconv.ItemReader, size uint, step uint, overlap uint, hole uint) windowReader {58 var bufferStep uint59 if overlap > step {60 bufferStep = step61 } else {62 bufferStep = overlap63 }64 return &partialWindowReader{65 reader: streamconv.NewLookaheadItemReader(reader),66 size: size,67 step: step,68 overlap: overlap,69 hole: hole,70 bufferStep: bufferStep,71 buffer: newWindowBuffer(overlap),72 bufferIndex: 0,73 reusedCount: 0,74 readCount: size,75 bufferedCount: overlap,76 }77}78func (r *partialWindowReader) Initialize(first bool) (err error) {79 if !first {80 err = skip(r.reader, r.hole)81 if err != nil {82 return83 }84 r.bufferIndex -= r.overlap85 r.reusedCount = r.overlap86 r.readCount = r.size - r.overlap87 r.bufferedCount = r.bufferStep88 r.err = nil89 }90 _, err = r.reader.Lookahead()91 return92}93func (r *partialWindowReader) ReadItem() (item io.Reader, err error) {94 if r.err != nil {95 return nil, r.err96 }97 defer func() {98 if err != nil {99 r.err = err100 }101 }()102 if r.reusedCount > 0 {103 item = bytes.NewReader(r.buffer.get(r.bufferIndex).Bytes())104 r.bufferIndex++105 r.reusedCount--106 return107 }108 if r.readCount == 0 {109 return nil, io.EOF110 }111 item, err = r.reader.ReadItem()112 if err != nil {113 return114 }115 r.readCount--116 if r.bufferedCount > r.readCount {117 buffer := r.buffer.get(r.bufferIndex)118 buffer.Reset()119 item = io.TeeReader(item, buffer)120 r.bufferIndex++121 r.bufferedCount--122 }123 return124}125func (r *partialWindowReader) Finalize() (err error) {126 return r.err127}128type completeWindowReader struct {129 reader streamconv.ItemReader130 size uint131 step uint132 overlap uint133 hole uint134 forwardLast bool135 buffer *windowBuffer136 bufferIndex uint137 lastItem io.Reader138 index uint139 err error140}141func newCompleteWindowReader(reader streamconv.ItemReader, size uint, step uint, overlap uint, hole uint) windowReader {142 forwardLast := overlap == 0143 bufferLength := size144 if forwardLast {145 bufferLength--146 }147 return &completeWindowReader{148 reader: reader,149 size: size,150 step: step,151 overlap: overlap,152 hole: hole,153 forwardLast: forwardLast,154 buffer: newWindowBuffer(bufferLength),155 bufferIndex: 0,156 index: 0,157 }158}159func (r *completeWindowReader) Initialize(first bool) (err error) {160 if !first {161 err = skip(r.reader, r.hole)162 if err != nil {163 return164 }165 r.bufferIndex -= r.overlap166 r.index = r.overlap167 r.err = nil168 }169 for i := uint(r.index); i < r.buffer.length; i++ {170 var item io.Reader171 item, err = r.reader.ReadItem()172 if err != nil {173 return174 }175 buffer := r.buffer.get(r.bufferIndex + i)176 buffer.Reset()177 _, err = io.Copy(buffer, item)178 if err != nil {179 return180 }181 }182 r.index = 0183 if r.forwardLast {184 r.lastItem, err = r.reader.ReadItem()185 if err != nil {186 return187 }188 }189 return190}191func (r *completeWindowReader) ReadItem() (item io.Reader, err error) {192 if r.err != nil {193 return nil, r.err194 }195 defer func() {196 if err != nil {197 r.err = err198 }199 }()200 if r.index == r.buffer.length {201 item = r.lastItem202 r.lastItem = nil203 r.err = io.EOF204 return205 }206 item = bytes.NewReader(r.buffer.get(r.bufferIndex).Bytes())207 r.bufferIndex++208 r.index++209 if (r.index == r.buffer.length) && (r.lastItem == nil) {210 r.err = io.EOF211 }212 return213}214func (r *completeWindowReader) Finalize() (err error) {215 return r.err216}217type multiWindowReader struct {218 reader windowReader219 subProgram streamconv.Transformer220 first bool221 transformed streamconv.ItemReader222 err error223}224func (r *multiWindowReader) ReadItem() (item io.Reader, err error) {225 if r.err != nil {226 return nil, r.err227 }228 defer func() {229 if err != nil {230 r.err = err231 }232 }()233 for {234 if r.transformed == nil {235 if !r.first {236 err = r.reader.Finalize()237 if err != io.EOF {238 if err == nil {239 err = fmt.Errorf("the previous window has not been fully read")240 }241 return242 }243 }244 err = r.reader.Initialize(r.first)245 if err != nil {246 return247 }248 r.first = false249 if r.subProgram != nil {250 r.transformed, err = r.subProgram.Transform(r.reader)251 if err != nil {252 if err == io.EOF {253 err = io.ErrUnexpectedEOF254 }255 return256 }257 } else {258 r.transformed = r.reader259 }260 }261 item, err = r.transformed.ReadItem()262 if err != io.EOF {263 return264 }265 err = nil266 r.transformed = nil267 }268}269type windowTransformer struct {270 subProgram streamconv.Transformer271 size uint272 step uint273 skipPartial bool274}275func (t *windowTransformer) Transform(src streamconv.ItemReader) (dst streamconv.ItemReader, err error) {276 var overlap, hole uint277 if t.step < t.size {278 overlap = t.size - t.step279 } else {280 hole = t.step - t.size281 }282 var reader windowReader283 if t.skipPartial {284 reader = newCompleteWindowReader(src, t.size, t.step, overlap, hole)285 } else {286 reader = newPartialWindowReader(src, t.size, t.step, overlap, hole)287 }288 dst = &multiWindowReader{289 reader: reader,290 subProgram: t.subProgram,291 first: true,292 }293 return294}295func NewWindowTransformer(subProgram streamconv.Transformer, size uint, step uint, skipPartial bool) streamconv.Transformer {296 return &windowTransformer{297 subProgram: subProgram,298 size: size,299 step: step,300 skipPartial: skipPartial,301 }302}...

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overlap.go

Source:overlap.go Github

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...79 if err != nil {80 return nil, err81 }82 defer file.Close()83 var unbufReader io.ReadCloser = file84 if isGzipped {85 unbufReader, err = gzip.NewReader(unbufReader)86 if err != nil {87 return nil, err88 }89 defer unbufReader.Close()90 }91 reader := bufio.NewReader(unbufReader)92 scanner := bufio.NewScanner(reader)93 var reads []read94 var seqBuf bytes.Buffer95 var name string96 for scanner.Scan() {97 line := scanner.Text()98 if strings.HasPrefix(line, ">") {99 if seqBuf.Len() > 0 {100 reads = append(reads, read{Label: name, Seq: seqBuf.String()})101 seqBuf.Reset()102 }103 name = strings.TrimSpace(line[1:])104 } else {105 seqBuf.WriteString(strings.TrimSpace(line))106 }107 }108 if seqBuf.Len() > 0 {109 reads = append(reads, read{Label: name, Seq: seqBuf.String()})110 }111 return reads, nil112}113func findOverlaps(i int, r runner.Runner, reads []read) ([]readPair, error) {114 step := int(len(reads) / r.NumRoutines())115 start := step * i116 end := start + step117 if end > len(reads) {118 end = len(reads)119 }120 var ret []readPair121 for i := start; i < end; i++ {122 tR := &reads[i]123 minLen := 40124 minLenRead := -1125 for j, pR := range reads {126 if i == j {127 continue128 }129 lenOverlap := suffixPrefixMatch(tR.Seq, pR.Seq, minLen)130 if lenOverlap > minLen {131 minLen = lenOverlap132 minLenRead = j133 } else if lenOverlap == minLen {134 minLenRead = -1135 }136 }137 if minLenRead != -1 {138 ret = append(ret, readPair{139 Left: tR, Right: &reads[minLenRead], Overlap: minLen,140 })141 }142 // maxLen := 40143 // var maxRead *read144 // matches, exists := prefixMap[tR.Seq[len(tR.Seq)-40:]]145 // if !exists {146 // continue147 // }148 // for j := range matches {149 // pR := &reads[j]150 // if tR.Label == pR.Label {151 // continue152 // }153 // lenO := suffixPrefixMatch(tR.Seq, pR.Seq, maxLen)154 // if lenO > maxLen {155 // maxLen = lenO156 // maxRead = pR157 // } else if lenO == maxLen {158 // maxRead = nil159 // }160 // }161 // if maxRead != nil {162 // ret = append(ret, readPair{163 // Left: tR, Right: maxRead, Overlap: maxLen,164 // })165 // }166 }167 return ret, nil168}169func suffixPrefixMatch(str1, str2 string, minOverlap int) int {170 if len(str1) < minOverlap || len(str2) < minOverlap {171 return 0172 }173 str2Prefix := str2[:minOverlap]174 str1Pos := -1175 for {176 str1Pos = index(str1, str2Prefix, str1Pos+1)177 if str1Pos == -1 {...

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compare_test.go

Source:compare_test.go Github

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...34func TestOverlapCount(t *testing.T) {35 var elements1, elements2 []Lift36 var actual int37 for _, v := range OverlapCountTests {38 elements1 = GoRead(v.elements1File)39 elements2 = GoRead(v.elements2File)40 actual = OverlapCount(elements1, elements2)41 if actual != v.expected {42 t.Errorf("Error in OverlapCount. Expected: %d. Actual: %d.", v.expected, actual)43 }44 }45}46func TestOverlapLength(t *testing.T) {47 var actual int48 for _, v := range OverlapTests {49 actual = overlapLength(v.A, v.B)50 if actual != v.expectedLength {51 t.Errorf("Error in OverlapLength. Expected: %d. Actual: %d.", v.expectedLength, actual)52 }53 }54}55func TestOverlapLengthSum(t *testing.T) {56 var elements1, elements2 []Lift57 var actual int58 for _, v := range OverlapCountTests {59 elements1 = GoRead(v.elements1File)60 elements2 = GoRead(v.elements2File)61 actual = overlapLengthSum(elements1, elements2)62 if actual != v.expectedSum {63 t.Errorf("Error in OverlapLengthSum. Expected: %d. Actual: %d.", v.expectedSum, actual)64 }65 }66}67var SortTests = []struct {68 inputFile string69 expectedByCoordFile string70 expectedBySizeFile string71 expectedByChromEndByChromFile string72}{73 {"testdata/sortInput.bed", "testdata/expectedSortByCoord.bed", "testdata/expectedSortBySize.bed", "testdata/expectedSortByChromEndByChrom.bed"},74}75func TestSortByCoord(t *testing.T) {76 var input, expectedCoord []Lift77 for _, v := range SortTests {78 input = GoRead(v.inputFile)79 expectedCoord = GoRead(v.expectedByCoordFile)80 SortByCoord(input)81 if !allAreEqual(input, expectedCoord) {82 t.Errorf("Error in SortByCoord.")83 }84 }85}...

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Read

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1func main() {2 overlap.Read()3}4func main() {5 overlap.Read()6}7func main() {8 overlap.Read()9}10func main() {11 overlap.Read()12}13func main() {14 overlap.Read()15}16func main() {17 overlap.Read()18}19func main() {20 overlap.Read()21}22func main() {23 overlap.Read()24}25func main() {26 overlap.Read()27}28func main() {29 overlap.Read()30}31func main() {32 overlap.Read()33}34func main() {35 overlap.Read()36}37func main() {38 overlap.Read()39}40func main() {41 overlap.Read()42}43func main() {44 overlap.Read()45}46func main()

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Read

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1import (2func main() {3 o.Read()4 o.Display()5}6import (7func main() {8 o.Read()9 o.Display()10}

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Read

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1import (2func main() {3 reader := bufio.NewReader(os.Stdin)4 fmt.Print("Enter text: ")5 text, _ := reader.ReadString('6 text = strings.Replace(text, "

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1func main() {2 o := overlap.NewOverlap()3 o.Read()4 fmt.Println(o)5}6import (7type Overlap struct {8}9func NewOverlap() *Overlap {10 return &Overlap{}11}12func (o *Overlap) Read() {13 fmt.Print("Enter x: ")14 fmt.Scanf("%f", &o.x)15 fmt.Print("Enter y: ")16 fmt.Scanf("%f", &o.y)17}18func (o Overlap) String() string {19 return fmt.Sprintf("Overlap: %f", math.Sqrt(o.x*o.x+o.y*o.y))20}21import (22func TestOverlap(t *testing.T) {23 o := overlap.NewOverlap()24 o.Read()25 if o.String() != "Overlap: 5.000000" {26 t.Errorf("Expected 5, got %s", o.String())27 }28}29import (30func TestOverlap(t *testing.T) {31 o := overlap.NewOverlap()32 o.Read()33 if o.String() != "Overlap: 5.000000" {34 t.Errorf("Expected 5, got %s", o.String())35 }36}37import (38type Overlap struct {39}40func NewOverlap() *Overlap {41 return &Overlap{}42}43func (o *Overlap) Read() {44 fmt.Print("Enter x: ")45 fmt.Scanf("%f", &o.x)46 fmt.Print("Enter y: ")47 fmt.Scanf("%f", &o.y)48}49func (o Overlap) String() string

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Read

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1import (2func main() {3 fmt.Println("Hello, playground")4 o.Read()5 fmt.Println("Read method of overlap class is called")6}7import (8func main() {9 fmt.Println("Hello, playground")10 o.Read()11 fmt.Println("Read method of overlap class is called")12}13import (14func main() {15 fmt.Println("Hello, playground")16 o.Read()17 fmt.Println("Read method of overlap class is called")18}19import (20func main() {21 fmt.Println("Hello, playground")22 o.Read()23 fmt.Println("Read method of overlap class is called")24}25import (26func main() {27 fmt.Println("Hello, playground")28 o.Read()29 fmt.Println("Read method of overlap class is called")30}31import (32func main() {33 fmt.Println("Hello, playground")34 o.Read()35 fmt.Println("Read method of overlap class is called")36}37import (38func main() {39 fmt.Println("Hello, playground")40 o.Read()41 fmt.Println("Read method of overlap class is called")42}43import (44func main() {45 fmt.Println("Hello, playground")46 o.Read()47 fmt.Println("Read method of overlap class is called")48}49import (

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1import "fmt"2func main() {3o.Read()4}5import "fmt"6func main() {7o.Display()8}9import "fmt"10func main() {11o.Add()12}13import "fmt"14func main() {15o.Sub()16}17import "fmt"18func main() {19o.Mul()20}21import "fmt"22func main() {23o.Div()24}25import "fmt"26func main() {27o.Mod()28}29import "fmt"30func main() {31o.Power()32}33import "fmt"34func main() {35o.Factorial()36}37import "fmt"38func main() {

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1import (2func main() {3 reader := bufio.NewReader(os.Stdin)4 fmt.Println("Enter text: ")5 text, _ := reader.ReadString('6 fmt.Println(text)7}

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