sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
a51666564c134c251cd84839c3cdef0ce6a6e908f58b2a19c42956e509870994 | Go | 2,694 | 67 | // Command Group: "BED Tools"
// Returns a bed file with the Score field containing the minimum distance from the end of the chromosome.
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/numbers"
)
func bedD... |
450c784c4ebdb571273c75a378a6ec5c14d4c29d9382d09eed3e9aaadf89b2a8 | Go | 2,697 | 139 | package numbers
import (
"testing"
)
var maxTests = []struct {
a int // first input
b int // second input
expt int // expected result
}{
{1, 2, 2},
{-1, 2, 2},
{-50, 2, 2},
{3, 7, 7},
{3, -7, 3},
{-3, -7, -3},
{100, 99, 100},
{100, -101, 100},
}
func TestMax(t *testing.T) {
for _, test := range ma... |
b3b4e3e688e590f0a3daed37469b46899a1d2c5fb9f996c472da45995f51bd32 | Go | 2,705 | 120 | package variant
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
)
type EffectorTest struct {
Effector
ExpectedEffect CodingChange
}
func equalEffects(a, b CodingChange) bool {
switch {
case a.Type != b.Type:
return false
case a.CodingPos != b.CodingPos:
return false
case a.ProteinPos != b.Prot... |
ff0955a748b1934c6510f8a36d7be379d76742277781eaa37779bc296ed23b3a | Go | 2,712 | 91 | package main
import (
"math"
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var bedMaxWigTests = []struct {
InputBed string
InputWig string
InputChromSizes string
OutputFile string
ExpectedFile string
MinFlag bool
AverageF... |
7ce48066c21c0ba4e81198453fd585acf26f73d63b95ee483d0eef0c4204467d | Go | 2,715 | 102 | package align
import (
"bytes"
"fmt"
"log"
"github.com/vertgenlab/gonomics/dna"
)
func colTypeToRune(a ColType) rune {
switch a {
case ColM:
return 'M'
case ColI:
return 'I'
case ColD:
return 'D'
default:
log.Fatalf("Error: unexpected value when converting colType to rune %d", a)
return '?'
}
}
... |
34a327e506df4848d741448500fd96cc9b56085bf45714fdaa461d39abdb03a9 | Go | 2,741 | 65 | package genomeGraph
import (
"sync"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/giraf"
"github.com/vertgenlab/gonomics/sam"
)
// Goroutine worker functions.
func RoutineFqToGiraf(gg *GenomeGraph, seedHash map[uint64][]uint64, seedLen int, stepSize int, scoreMatrix [][]int64, inputChan ... |
289222ea193a95292be86c5906c2844f8c475ea6ad5858fe908286de18854601 | Go | 2,744 | 50 | package binaryGiraf
// Package binaryGiraf provides functions for reading and writing binary giraf files
import (
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna/dnaThreeBit"
)
// The structs in this file are only present for documentation and should not be used
// Compressed with BGZF ... |
d2c65d6abaed132c299f58b13c62a9d3462854e28aed7b4fc0c6e9ff3589fd1b | Go | 2,745 | 92 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"path/filepath"
"strings"
"testing"
)
var BedSplitTests = []struct {
Mode string
InFile string
OutDir string
GzipOut bool
ExpectedDir string
}{
{Mode: "byName",
InFile: ... |
d57ba3ba4934b9d72737da9c337cb90703abe0aadbca8d0849b2d00aaa0d8d34 | Go | 2,766 | 86 | // Command Group: "Data Simulation"
// Contains functions for simulating VCF data
package main
import (
"flag"
"fmt"
"log"
"math/rand"
"github.com/vertgenlab/gonomics/simulate"
)
func simulateVcf(s Settings) {
rand.Seed(s.SetSeed)
simulate.VcfToFile(s.Alpha, s.NumAlleles, s.NumSites, s.OutFile, s.BoundAlpha,... |
5e322ef3b8279f6805f06d59bfa5dd2381055dcfd5ac25f2fb6c8e62fda1a517 | Go | 2,768 | 78 | package sketch
import (
"image"
"image/color"
"testing"
)
// TestHLine tests the HLine function by drawing a horizontal line and checking if the expected color is set at each pixel.
func TestHLine(t *testing.T) {
img := image.NewRGBA(image.Rect(0, 0, 10, 10))
col := color.RGBA{255, 0, 0, 255}
HLine(img, 2, 7, ... |
441dcbf1d812868c44ecc61d8ae93a4eafaf66cea37a7c953c1deb8c6110f8cc | Go | 2,770 | 100 | package main
import (
"flag"
"fmt"
"log"
"os"
"strings"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/genomeGraph"
"github.com/vertgenlab/gonomics/giraf"
)
// TODO: View feature needs some work.
type ViewExe struct {
Cmd *flag.FlagSet
GirafFile string
SamFile string
}
va... |
62a935917f4208eaa202c9367c32b1eeb8b9bace03ad391b9c819746bd723fdf | Go | 2,780 | 103 | // Command Group: "Data Conversion"
// Converts sam or bam to wig
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/convert"
"github.com/vertgenlab/gonomics/sam"
"github.com/vertgenlab/gonomics/wig"
)
type... |
8232b7f155fdaf5dc39ff875fb2c1de9b6f9e19893a4a714de0a12fd14f11b8c | Go | 2,784 | 81 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
)
var MultiFaExtractTests = []struct {
inputFile string
outputFile string
expectedFile string
removeGaps bool
bed string
start int
end int
out1 st... |
0f4d7e812a03a14c3339b16ea9f5143c41bc0ee05443fdd2c0edd96ce2ee99ef | Go | 2,809 | 78 | package maf
import (
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
)
func setupBlankAln(ref fasta.Fasta, species []string) []fasta.Fasta {
var answer []fasta.Fasta
answer = append(answer, ref)
answer[0].Name = species[0]
for i := 1; i < len(species); i++ {
answer = append... |
c663dccd03ed676bb3f35fbdb7bc4411b373e8f94430bf7cde2571fb28a839a3 | Go | 2,810 | 90 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var NonCodingTests = []struct {
TreeFile string
FastaFile string
OutFile string
SetSeed int64
NumNodes int
GammaAlp... |
dd36456a2c9bc1acffc79747b848f7ab574da887c85f132968a51681a433f2c0 | Go | 2,810 | 101 | package sam
import (
"fmt"
"github.com/vertgenlab/gonomics/exception"
"io"
"strings"
)
// SamPE is struct that contains 2 paired end Sam entries as well as a slice of Sam that represents all supplementary
// alignments for the read-pair
type SamPE struct { //TODO: rename from A/B to something more informative
R1... |
cb31326bed8576b3d36d407d02da586ab223d1778dbb3dbbdcce8e650f308735 | Go | 2,811 | 86 | package genomeGraph
import (
"log"
"github.com/vertgenlab/gonomics/align"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
)
func nmMatrixSetup(size int64) ([][]int64, [][]rune) {
m := make([][]int64, size)
trace := make([][]rune, size)
for id... |
3c0b1b647999aefecef6202513343551047fbf40e0ce53ab4e066160a5b9db24 | Go | 2,821 | 102 | package main
import (
"encoding/csv"
"os"
"strings"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var VcfFormatTests = []struct {
InFile string
OutFile string
ExpectedFile string
EnsemblToUCSC bool
UCSCToEnsembl bool
FixVcfRecords bool
Ref ... |
1d80ab26d0101e5488a4c0c05d5ca26da8aa55c633aae951312dd2c1c2ce49c6 | Go | 2,830 | 70 | package fastq
import (
"fmt"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
// SingleCellPair is a struct that contains single-cell sequencing information, including a pairedEnd read, barcode, and UMI.
type SingleCellPair struct {
Reads ... |
ccf420b61fbded96dda6bd6819df0d267eae46c564aa03f4f750842bb1002122 | Go | 2,833 | 81 | // Command Group: "FASTA and Multi-FASTA Tools"
// Concatenate multiFa alignment files by sequence. Accepts an arbitrary number of input fasta files
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"... |
e0d2d5a254ea6625a2a7dc454de680235da2a51a01226ec5066cff2db39572bd | Go | 2,856 | 87 | package main
import (
"github.com/vertgenlab/gonomics/fileio"
"testing"
)
/*
Testing files were generated with the following commands in gonomics v1.0.0
~/go/bin/randSeq -lenSeq 1000 -numSeq 1 -setSeed 5 myRandSeq.fa
~/go/bin/simulateSam -coverage 1.0 -flatErrorRate 0.01 -setSeed 9 myRandSeq.fa test1.unsorted.bam... |
7d745cc240ad1ae7e895a0de4241eb96a9819eb708f24586598f95f279b198ee | Go | 2,857 | 96 | package lift
import (
"testing"
"github.com/vertgenlab/gonomics/bed"
)
var OverlapTests = []struct {
A bed.Bed
B bed.Bed
expected bool
expectedLength int
}{
{A: bed.Bed{"chr4", 1, 10, "", 0, bed.Positive, 3, nil}, B: bed.Bed{"chr4", 4, 12, "", 0, bed.Positive, 3, nil}, expected... |
53cec959479b7925b8a6f1b79f0e1bcda308a14e1c35b6d3b4e93419bb2b737f | Go | 2,858 | 99 | // Command Group: "BED Tools"
// Combines overlapping bed entries, keeping max score. Output will be sorted by genome coordinate
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonom... |
bd49c853a5dbc7ce57b2d62125531d8bdd2e1d5a6e921d428b89952f7304c315 | Go | 2,858 | 109 | package fileio
import (
"bytes"
"io"
"os"
"github.com/vertgenlab/gonomics/exception"
)
// magic number that identifies a gzip file.
var magicGzip = []byte{0x1f, 0x8b}
// IsGzip checks if the magic gzip number is
// present at the start of the input io.ReadSeeker.
// After check for the magic number, IsGzip
// s... |
0225499192a7798ece70ce5e009ffb1ff6ec6f7ba63ce1cb1e854e58edda831f | Go | 2,859 | 87 | // Command Group: "Data Conversion"
// Converts bed score to wig
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/convert"
"github.com/vertgenlab/gonomics/wig"
"log"
"math"
)
type Settings struct {
Method ... |
07358e2e2cb176453ce22a773d91819f7637b2cb117186e77cb7f6e65fdb57ce | Go | 2,866 | 85 | // Command Group: "General Tools"
// Perform functional enrichment analysis by associating genomic regions
// with their nearest gene in 3d space using bedPe contact sites.
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/bed/bedpe"
"github.com/vertgenlab/go... |
e51d3e4e9b98cb03046ab1604012b98dc68234fe96067ae4e4f605fd3fba64c2 | Go | 2,872 | 104 | // Command Group: "VCF Tools"
// Options alter VCF formatting
package main
import (
"flag"
"fmt"
"log"
"strings"
"github.com/vertgenlab/gonomics/convert"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fil... |
5bc72114c49ea526fca9488c75dea4d18e3c26794ac8e1b3f1099869dafb9044 | Go | 2,879 | 94 | // Command Group: "BED Tools"
// Generates ideogram txt file from a bed
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/numbers/parse"
"log"
"strings"
"github.com/vertgenlab/gonomics/fileio"
)
type IdeogramPoint struct {
Chrom string
Position... |
c9358eee7b8764d37350b25a2b1fd57b600df2f9377f429940794ea83a887158 | Go | 2,893 | 140 | package main
import (
"io/ioutil"
"os"
"testing"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/dna/dnaTwoBit"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/genomeGraph"
)
func TestSortOrder(t *testing.T) {
sortedGraph := test(MakeTestGraph())
correctOrder ... |
914062fc177ad895952968f6e4d29ae39d2f3f095984b8d97d0d3a32b9e19b1c | Go | 2,904 | 144 | package bgzf
import (
"bytes"
"compress/gzip"
"crypto/md5"
"encoding/binary"
"fmt"
"io"
"log"
"os"
"testing"
)
func TestWrite(t *testing.T) {
b := NewBlock()
r := NewBlockReader("testdata/test.bam")
tmpfile, err := os.Create("testdata/tmp.bam")
if err != nil {
log.Panic(err)
}
w := NewBlockWriter(tmp... |
1334a62e9859efb95ebf449f665781de8170226feaba31f791dc0ecbd4622619 | Go | 2,924 | 106 | // Command Group: "FASTQ Tools"
// Options alter fastq file formatting
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/fileio"
)
func fastqFormat(s Settings) {
if !s.PairedEnd {
log.Fatalf("fastqForma... |
a95aa8905961ee6e986915d47a924eb8eca92a383cab41d71bb4fe5b736bf4bb | Go | 2,926 | 82 | package gtf
import (
"os"
"testing"
)
var c1 Cds = Cds{Start: 173477398, End: 173477492, Score: -1, Frame: 0}
var f FiveUtr = FiveUtr{Start: 173477335, End: 173477397, Score: -1}
//var e1 Exon = Exon{Start: 173477335, End: 173477492, Score: -1, ExonNumber: "\"1\"", ExonID: "\"NM_004905.1\"", Cds: &c1, FiveUtr: &f}... |
02fcc5a9047ff81a045eda1cb37386240e6b5d8755a2f955b751e78e03597d6e | Go | 2,938 | 117 | package main
import (
"fmt"
"sync"
"testing"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/interval"
"github.com/vertgenlab/gonomics/vcf"
)
const (
testSelectFile string = "testdata/imbalance.bed.gz"
testInputFile string = "testdata/imbalan... |
5f1f0da11dbf1955ba0e75011327da7b1e1122444b6021a8acb90368aa6f2fd3 | Go | 2,940 | 100 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var bedToWigTests = []struct {
InFile string
RefFile string
OutFile string
ExpectedFile string
Method string
DefaultValue float64
UseRange ... |
0b6245ddf46a824f45442c61bab12942f0b57cf6a7f6e01988a77add96e75ac3 | Go | 2,947 | 78 | package dnaThreeBit
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
)
//func BasesToUint64(seq []dna.Base, start int, end int, padding ThreeBitBase) uint64 {
//func basesToUint64WithOffset(seq []dna.Base, start int, end int, padding ThreeBitBase, offset int) uint64 {
//func GetThreeBitBase(fragment *ThreeB... |
bbd3076be24ecd785b92f8707dd5e13e8a59a7bbb0f52c8464fda5549af6b12d | Go | 2,960 | 107 | // Command Group: "FASTA and Multi-FASTA Tools"
// Pull sub-sequence from multiple Fasta alignment for each entry
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/numbers/parse"
"log"
)
func multiFaExtract(s Settings)... |
a7d4bf71d61deaac320ccf498d1cdb46598fce187c23754a5ee43cedb4f15b84 | Go | 2,973 | 116 | package obo
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var ToDotTests = []struct {
InFile string
OutFile string
ExpectedFile string
}{
{InFile: "testdata/test.obo",
OutFile: "testdata/out.dot",
ExpectedFile: "testdata/expect... |
dd60e1c15e3bc753765067d4aef1a81fc5be86c2723f0d8d6a63e3ab0f5dfc43 | Go | 2,977 | 130 | package interval
import (
"fmt"
"log"
)
const (
xMin = 0
xMax = 10_000_000_000 // maximum size of genome
)
// TestValidRelationship tests that the input relationship string for a query is supported.
func TestValidRelationship(op string) bool {
switch op {
case "o":
case "oi":
case "d":
case "di":
case "m":... |
c79b54425cc62b560c44680eaa7bdce2a4464f80bda0fef170d48e0e28b321ae | Go | 2,993 | 102 | package interval
import (
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
"os"
"testing"
)
var CoordsToStringTests = []struct {
I Interval
Expected string
}{
{I: bed.Bed{Chrom: "chr1... |
27b2a032f8a031c713f4eb025bf3ce0b198317f69d7a25a9f8b4fc923e333692 | Go | 3,022 | 98 | // Command Group: "Data Conversion"
// Convert axt alignments to sam format
package main
import (
"flag"
"fmt"
"log"
"sync"
"github.com/vertgenlab/gonomics/axt"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/go... |
4304f470fd642df4bd1518692565d4c9b8cf7f70e56cd0d321f556d233affbb6 | Go | 3,044 | 95 | // Copyright 2020 Google Inc.
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in wr... |
a03930f52fb147e6a550d57746daa0097a6d21892f359f9731152a4d41f5240a | Go | 3,065 | 129 | package gtf
import (
"strings"
)
// AllAreEqual returns true if all of the entries in a GTF map contain the same information, false otherwise.
func AllAreEqual(a map[string]*Gene, b map[string]*Gene) bool {
if len(a) != len(b) {
return false
}
for k := range b {
if _, ok := a[k]; !ok {
return false
} els... |
1ef2f85c7b392e4c547251401afd844c97d90b7b058824e5012f4eda1793ff20 | Go | 3,070 | 88 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/motif"
"log"
)
type Settings struct {
InFile string
MatrixFile string
OutFile string
MatrixFileType string
PropMatch float64
Pseudocounts float64
Outp... |
f22c24a4c250920ea1ad5d4a4f162a3a7a0e95c96d7adf889d9e69149b9dc41e | Go | 3,072 | 84 | package simulate
import (
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/numbers"
"log"
)
// CountWindows counts the total viable windows of length regionLength in the sequence searchSpace
func CountWindows(searchSpace []bed.Bed, regionLength int) int {
var length, totalWindows int
for i :=... |
9338bcd29b55140c32113f9d07ca81af3e4bd1807ab2ebdc21f047ce4f84fc23 | Go | 3,083 | 106 | package bedGraph
import (
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers/parse"
"io"
"strings"
"sync"
)
// BedGraph stores information about genomic regions, including their location and an associated float DataValue.
// As with ... |
beaee15f144b42e2dd511a309cc47ca141f4524b1ffb31bf2e56cb2f9d376a30 | Go | 3,094 | 87 | package dnaThreeBit
import (
"log"
"math/bits"
)
// countRightMatches counts the number of perfectly matching bases between seqOne and seqTwo, starting
// a position startOne in seqOne and startTwo in seqTwo. The slices must be encoded with the threeBit format
// and in register with each other. The first compari... |
10ff3bae805626110dd14b8aaba8a860a098fc5d0a03bbc25abf1e419c2fc3f6 | Go | 3,109 | 101 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var BranchLengthsMultiFaBedTests = []struct {
Chrom string
InFaFile string
InBedFile string
VelLengthBedFile string
Init... |
cac87b1b0c04a0b934cce556c1fe5c4e73610289517be92b18775f37df2df845 | Go | 3,127 | 134 | package logspace
import (
"math"
"testing"
)
func TestToBase10(t *testing.T) {
var inputs = []float64{0, 1.5}
var observed float64
for _, v := range inputs {
observed = ToBase10(math.Log(v))
if observed != math.Log10(v) {
t.Errorf("Error in ToBase10. Expected: %v. Observed: %v.\n", math.Log10(v), observed... |
d2fb559419987568a1516c39e7206e69e3ef978e323d84a505e35e0bd82c1c6f | Go | 3,134 | 69 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/bed/bedpe"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/ontology"
"github.com/vertgenlab/gonomics/ontology/gaf"
"github.com/vertgenlab/gonomics/ontology/obo"
"log"
)
func onto... |
6e8cba5f6ca3f09df6280d00b3ad3939e5a49ea07ccf36c0f51dcd2a42d3b786 | Go | 3,136 | 128 | package dna
import (
"log"
)
// Count returns the number of each base present in the input sequence.
func Count(seq []Base) (ACount int, CCount int, GCount int, TCount int, NCount int, aCount int, cCount int, gCount int, tCount int, nCount int, gapCount int) {
for _, b := range seq {
switch b {
case A:
ACoun... |
d41103a96eb3c5a637f0c18ba0399d3d3e22b824d7addc1a7d802eb455d9daba | Go | 3,164 | 99 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/wig"
"log"
"math"
"os"
)
// StatsSettings defines the usage settings for the wigTools stats subcommand.
type StatsSettings... |
bbb80875b3e2c4bee4d47c28b2be4c3a14525d0ec05a77f6625a1635f71e1fe4 | Go | 3,176 | 93 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/motif"
"log"
"math/rand"
"os"
)
// ShuffleSettings defines the usage options for the pwmTools shuffle subcommand.
type ShuffleSettings struct {
InFile stri... |
f6209c4b4290cfa7758fad34bb86afbab367c6f7e7b24b68947c3f20f2ef18ca | Go | 3,186 | 109 | package main
import (
"bytes"
"log"
"net/http"
"os"
"strings"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/vcf"
)
func TestVcfWebAnnotate(t *testing.T) {
if !pingServer() {
return
}
testfile := "tmp_testfile.vcf"
vcfs, he... |
e9e771987a0a25eb41603a237a903f3a25ed584ae7e59d32290ed913a2498704 | Go | 3,218 | 124 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"math"
"os"
"testing"
)
var BedpeFilterTests = []struct {
InFile string
OutFile string
ExpectedFile string
MinScore int
MaxScore int
MinDistance int
MaxDistance int
... |
34708b9b4e2460cf9431f35d06a5cee74a1b41e4fc663f9a1da8ad72dce6e61e | Go | 3,220 | 113 | // Package hic is written to process output from the aidenlab functions
// straw function: https://github.com/aidenlab/straw
// note: this package only reads and does not write this file type
package hic
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenl... |
1a01ca88dcece115a0f00da1ffaed42e57186e2ec01d9ff96aa6c7f8cc4955a3 | Go | 3,221 | 87 | package ontology
import (
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/bed/bedpe"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
func TestFill3dSpace(t *testing.T) {
var genes = []bed.Bed{{C... |
fa6ad52fb65e12c96ae920d97e303e7987e39faf5c58671f873a262f10e963e1 | Go | 3,231 | 99 | package chain
import (
"log"
"strings"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/numbers"
)
// OverlapChainBed returns true if the provided chain and bed overlap
// in genomic coordinates. If check target is true, this calculation
// is done on the chain's target, and otherwise on the... |
ac357c1b015d678aad0e44ce4b60597746a9b3a86c3a46d08f7dfd6732159c20 | Go | 3,239 | 131 | package expandedTree
import (
"fmt"
"math"
"testing"
)
func initializeMyRoot() *ETree {
var myRoot, firstLeft, firstRight, secondLeft, secondRight ETree
myRoot = ETree{
Name: "myRoot",
Up: nil,
Left: &firstLeft,
Right: &firstRight,
}
firstLeft = ETree{
Name: "firstLeft",
BranchLength: ... |
a21fa422de712382e016a651136d6fccf238854f0d66fcc0917a85c786c56e23 | Go | 3,245 | 83 | // Command Group: "Data Conversion"
// Generates a VCF file from an input pairwise or three-way multiFa alignment with the first entry as the reference
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/convert"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fa... |
9a76197198d21b464578d7d6a92013ae0ce1a2677bf0a8b3886488006feff46a | Go | 3,263 | 111 | package fasta
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/dna"
)
var seqOneA = dna.StringToBases("ACGTacgTCATCATCATTACTACTAC")
var seqOneB = dna.StringToBases("acgtACGTACGT")
var seqOneC = dna.StringToBases("ACGTACGTACGTT")
var readWriteTests = []struct {
filename string // input
data []Fasta
}{... |
3f92885ac9fed63d49e7db8e15cd1bcbb7faf48270eabd575077bdd99456a89b | Go | 3,278 | 75 | // Command Group: "Statistics & Population Genetics"
// Performs maximum likelihood estimation of selection on variants from an input VCF format file
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/popge... |
e9d9bb922d2c81da17ab2fa95b49dee25acbe762fd24e7d2248ee5674f1b8199 | Go | 3,281 | 82 | package main
import (
"log"
"path/filepath"
"strings"
"sync"
"time"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/genomeGraph"
"github.com/vertgenlab/gonomics/giraf"
"github.com/vertgenlab/gonomics/sam"
)
func GswToGirafPair(ref *genomeGraph.... |
67b972ef0e72652bff6b53916e02ee6928619f4aa1e0fd45becbfd8f15f6deed | Go | 3,285 | 113 | package motif
import (
"fmt"
"os"
"testing"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var ScoreWindowTests = []struct {
MatrixFile string
Seq [][]dna.Base
AlnStart []int
ExpectedScores [][]float64
Expected... |
db669f156a83b9375daeac0b1dccdeb29ca62898477078af3cd61383cbb7fd3c | Go | 3,290 | 81 | package lift
import (
"github.com/vertgenlab/gonomics/axt"
"github.com/vertgenlab/gonomics/numbers"
"testing"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/interval"
)
var ReadingTests = []struct {
Infile string
Expected []Lift
}{
{"testdata/elements1.bed", []Lift{bed.Bed{Chrom: "chr... |
b19d694248b18595aaa5b5f49f24c1ad44de4b62111f041c7af9a23f1df67cfd | Go | 3,319 | 79 | package numbers
import (
"testing"
)
func TestRandExp(t *testing.T) {
expectedMean := 1.0
expectedVariance := 1.0
var input []float64
input = make([]float64, 100000)
for i := 0; i < 100000; i++ {
input[i], _ = RandExp()
}
ave := AverageFloat64(input)
variance := VarianceFloat64(input)
if ave < expected... |
888dcc048ac09f87d6502b0d33c21f10df2954133103e491fee7575fdfd4846a | Go | 3,325 | 55 | package fastq
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
)
func TestTrimmingBarcodes(t *testing.T) {
var nameOneFwd string = "ST-E00545:471:HVJ32CCXY:2:1101:6705:1538_UMI:AGGTGG_BX:NTCGGACGTGGGAAGG"
var bxOne []dna.Base = dna.StringToBases("NTCGGACGTGGGAAGG")
var umiOne []dna.Base = dna.StringToBas... |
e9fe6a3c4da6470f1f01fef1353cb63d7554065380c3bb52d43da06150a756f3 | Go | 3,327 | 236 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var StatCalcTests = []struct {
Args []string
Normal string
Binomial string
Poisson string
Beta string
Gamma string
SampleAfs string
SampleBeta... |
14e72e307deaff3fe4cf87d95a9c4932d7389162849bb69c5f234373362431be | Go | 3,341 | 147 | // Command Group: "BED Tools"
// Performs comparative arithmetic operations on float values in bed files
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers/parse"
"log... |
3011897f97c80731b2e7cc4d62e5afa0a852974cbdef1d4c8521f841c9f29e34 | Go | 3,348 | 68 | package bed
import (
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
"log"
"strings"
)
// ToLower converts bases in a fasta sequence to lowercase in specified bed regions, where the bed chrom name matches the fasta record name
func ToLower(records []fasta.Fasta, regions []Bed, ignoreEx... |
71dc8386832d20bff0bc64f4a7fccb6fe82f7b132a2521d42fc682c9b42c8286 | Go | 3,364 | 124 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var ToBedTests = []struct {
InFile string
OutFile string
ExpectedFile string
Tss bool
FirstTwoCodonBases bool
ChromSizesFile string
Merge... |
9ae2bfae0d74f2ad262d1ab8c85b2ec41e1f19085785ddfaa2a131b2ba02d43f | Go | 3,366 | 88 | package popgen
import (
"log"
"math/rand"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/vcf"
)
// SimulateSegSite returns a segregating site with a non-zero allele frequency sampled from a stationarity distribution with selection parameter alpha.
// the second returns true if the site ... |
4d8214e59ccef3e5df08b414f0d1085dc84d3a87302ab6fa71efed4ef509e539 | Go | 3,371 | 89 | // Package popgen contains functions for analyzing population genetic statistics from variation or alignment data.
package popgen
import (
"math"
"github.com/vertgenlab/gonomics/align"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
"github.com/ve... |
f92ded70b1153077b3c7949e80008903e75cd21255ae21c343753fa43da99a65 | Go | 3,393 | 132 | // Command Group: "Sequence Evolution & Reconstruction"
// Determine the mutation spectrum for divergent sites in each region of an input bed file
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"g... |
c0564ef2a6ea722eaae6add796b8bad3aa8035a063108dd428759e13972f6f31 | Go | 3,402 | 103 | package dna
import (
"log"
"math"
)
// nnTable is a map that has nearest neighbor dinucleotides and they're corresponding deltaH () and deltaS () values, respectively.
// Entropy/enthalpy values were empirically determined in: Allawi and SantaLucia (1997), Biochemistry 36: 10581-10594
var nnTable = map[string][]flo... |
c9426defe2e29ccf9638f2ce770d11c28d1e37e3c3ec5f9737c7178533f27937 | Go | 3,405 | 131 | package popgen
import (
"fmt"
"io"
"strconv"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/vcf"
)
type WrightFisherSettings struct {
PopSize int
MutRate float64
NumGen int
G... |
476bb789ed1489591b4b3ca9dae2ee5f72e10800461955dab43d07043be9f0d3 | Go | 3,425 | 93 | package simulate
import (
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/expandedTree"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers/parse"
"log"
"math/rand"
"strings"
)
// Jukes-Cantor matrix, medium distance.
var ... |
754cbb8a361feb241c47554acc37bb8d9ca615c4843593f7ff4b3d68ede0489e | Go | 3,427 | 95 | package numbers
import (
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers/parse"
"log"
"math"
"sort"
"strings"
)
// McmcTrace is a general struct for Mcmc trace output. Used for discarding burn-in and calculating the mean and credible interval.
type McmcTrace struct {
Parameter [... |
5b466bfab8058b0cf1e1f8d0d7dc23332d7ef086d3b2fdbd68e1e9ea2ee14f61 | Go | 3,433 | 128 | package fileio
import (
"bytes"
"testing"
)
func TestByteioReader(t *testing.T) {
answer := ezReaderTest("testdata/big.fa.gz")
reader := NewByteReader("testdata/big.fa.gz")
var i int = 0
for line, done := ReadLine(reader); !done; line, done = ReadLine(reader) {
if line.String() != answer[i] {
t.Errorf("Err... |
c3bb6c88d74c447dd0e00d2432c51625a47f1956e1b6d4da6c2351d642ea48db | Go | 3,445 | 97 | package vcf
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
)
var AncestorAlleles []dna.Base = []dna.Base{dna.A, dna.T, dna.G, dna.C, dna.A, dna.A, dna.C}
func TestVcfQueryAncestor(t *testing.T) {
reader, _ := GoReadToChan("testdata/AncestorTest.vcf")
var input []... |
7e57be6d1fd5460bdb1898c93536f9ccadcc82375f095412fbb0d493a2dda055 | Go | 3,448 | 76 | package main
import "github.com/vertgenlab/gonomics/sam"
// CacheStruct contains a collection of all caches used for the likelihood and
// prior calculations in samAssembler.
type CacheStruct struct {
DiploidBasePriorCache [][]float64
DiploidIndelPriorCache []float64
HaploidBasePriorCache [][]float64
HaploidInd... |
dd99cb8a60e281003c0eeb9ba603631fea4475af74936ce3a965862b0fd0d01a | Go | 3,466 | 122 | // Command Group: "Data Conversion"
// Find and replace gene IDs with gene names according to an input table or preset NCBI RefSeq / ENSEMBL ID conversion tables
package main
import (
"flag"
"fmt"
"log"
"strings"
"github.com/vertgenlab/gonomics/cmd/geneIdToName/presets"
"github.com/vertgenlab/gonomics/exceptio... |
df182640e0bc667f061d10ab9707610f2f4a8438d8e9a941ceba3e61d00d3617 | Go | 3,475 | 114 | package wig
import (
"log"
"math"
//DEBUG: "fmt".
"math/rand"
"sort"
"strings"
"github.com/vertgenlab/gonomics/numbers"
)
// isEqual returns true if two Wig data structures contain the exact same data values and returns false otherwise.
func isEqual(alpha Wig, beta Wig, precision float64) bool {
if strings.... |
691524a0080c79015498364d9ea3d4b7b331a7283e2ec08b60b22d788044cf5b | Go | 3,507 | 116 | package bed
import (
"github.com/vertgenlab/gonomics/numbers"
"log"
)
// TrimSlice trims each element in a slice of bed entries by an input left and right amount.
func TrimSlice(b []Bed, trimLeft int, trimRight int) {
for i := range b {
b[i] = Trim(b[i], trimLeft, trimRight)
}
}
// Trim shortens bed entries on... |
4304e90eb353f136ec99222f71d5410c9bba9e5421aacd319aff4f3485d14f6a | Go | 3,508 | 114 | package lift
import (
"testing"
)
var ElementOverlapProbabilityTests = []struct {
elements1File string
elements2File string
NoGapRegionsFile string
Expected []float64
}{
{"testdata/EnrichmentElement1.bed",
"testdata/EnrichmentElement2.bed",
"testdata/EnrichmentNoGap.bed",
[]float64{0.0578231... |
e2a00bacf767b355067b9622ed3bc7f64df1754e390cd96d069b80569eec6967 | Go | 3,525 | 48 | package simulate
import (
"fmt"
"github.com/vertgenlab/gonomics/expandedTree"
"math/rand"
"strings"
"testing"
)
var ETreeTests = []struct {
NumNodes int
GammaAlpha float64
GammaBeta float64
SetSeed int64
Expected string
}{
{NumNodes: 9,
GammaAlpha: 2,
GammaBeta: 20,
SetSeed: 14,
Expecte... |
1b12327a195b11647805f3e6a057ab99d8a65f2711ba3f77294ee5e5f0f497d1 | Go | 3,534 | 90 | package gtf
import (
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/vcf"
)
// FilterVariantGtf takes a vcf record, a gene list from a gtf, ChromInfo to know the length of chromosomes, and whether the function... |
5802c8e41f7c09cc90f57476c1f5b63cfa842865e1f8ad71e2d06b3f89124842 | Go | 3,550 | 154 | package vcf
import "testing"
var VcfMethodsTests = []struct {
v Vcf
expectedChr string
expectedStart int
expectedEnd int
newChr string
newStart int
newEnd int
}{
{v: Vcf{Chr: "chr1", Pos: 2, Ref: "A", Alt: []string{"T"}},
expectedChr: "chr1",
expectedStart: 1,
expect... |
55f2debc559cd773fcd12403f20c199e28a8a44852a519e3af91a34f5cd974c3 | Go | 3,551 | 86 | // Command Group: "Data Simulation"
// Simulate a multiallelic, haplotic Wright-Fisher population (discrete, non-overlapping generations)
package main
import (
"flag"
"fmt"
"log"
"math/rand"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/popgen"
)
func simulateWrightFisher(outFile stri... |
79e055d50819c1750225a5e301944147482a1966e19d63c8ec06f0576e8a5cce | Go | 3,572 | 96 | package sam
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
)
var HaploidCallFromPileTests = []struct {
P Pile
RefBase dna.Base
Gamma float64
Delta float64
Epsilon float64
Kappa float64
Lambda float64
Expected HaploidCall
}{
{P: Pile{CountF: [13]int{30, 0, 0, 0, 0, 0, 0, 0, 0, ... |
362063155df8ced30c015660f7955e8192e58307ea7636a597a4bfc2687dab6f | Go | 3,585 | 89 | // Command Group: "Statistics & Population Genetics"
// Returns allele frequency spectrum information in a text file for graphing
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/popgen"
)
type Settings ... |
afe6123d6ea15db635e17b6332e56a8892d92e84f59da5f7d753cbdf91b6f6c8 | Go | 3,590 | 126 | package vcf
import (
"io"
"strconv"
"strings"
"github.com/vertgenlab/gonomics/dna"
)
// String implements the fmt.Stringer interface for easy printing of Vcf with the fmt package. No trailing newline character
// is added to the end of the string
func (v Vcf) String() string {
// TODO: Consider reducing allocat... |
baa912a9a3b3343036fcd783df060a91e5496c4a00627e03901a1f648a05c880 | Go | 3,606 | 91 | package cigar
import (
"testing"
)
func TestAppend(t *testing.T) {
tests := []struct {
alpha []Cigar
beta Cigar
expected []Cigar
}{
{[]Cigar{{2, Deletion}, {30, Match}}, Cigar{20, Match}, []Cigar{{2, Deletion}, {50, Match}}},
{[]Cigar{{1, Deletion}, {10, Match}}, Cigar{2, SoftClip}, []Cigar{{1, De... |
7748fad533c7f388d468cdf075e011c321377b910c665264730fa890f082fdc2 | Go | 3,613 | 165 | package genomeGraph
import (
"fmt"
"log"
"testing"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/dna/dnaTwoBit"
"github.com/vertgenlab/gonomics/giraf"
)
// TestGraph Structure
// n2 e0 = 1
// e1/ \e2 e1 = 0.05
/... |
b331adc47bd84b1e435677bf57209e81ec0e4a2edfa864330048b5f757bde3d4 | Go | 3,624 | 125 | package main
import (
"flag"
"fmt"
"os"
)
// Genome Graph Gonomics.
func usage() {
fmt.Print(
"GSW - Graph Smith Waterman:\n\nGenome Graph Software\n" +
"Author: Eric Au\n\tCraig Lowe\n\n" +
"Vertebrate Genetics Laboratory: http://www.vertgenlab.org\n" +
"Source code: https://github.com/vertgenlab/gono... |
3f97738c4d144a76340af08b75f7061978f249ee95b28d59d6b21c14e3d19f09 | Go | 3,626 | 157 | package vcf
import (
"log"
"sort"
"strings"
//"github.com/vertgenlab/gonomics/dna".
"github.com/vertgenlab/gonomics/numbers"
)
const debugMode = 0 //set debugMode to 1 to enable prints
// CompareCoord compares two VCF structs by Pos for sorting or equality testing.
func CompareCoord(alpha Vcf, beta Vcf) int {
... |
da343584caeac8f07bc83e8f39dfcd831ab0d4f8511e88509a1a70b2624c5aac | Go | 3,626 | 129 | // Command Group: "SAM Tools"
// Count bases from sequencing data
package main
import (
"flag"
"fmt"
"log"
"strings"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/sam"
)
func usage() {
fmt.Print(
"pi... |
d8dd452d6e0ba4c37c56d5bac5c06a41b0fb30970f8a1cda25e5bf069c3873a5 | Go | 3,647 | 95 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/simulate"
"log"
"math/rand"
"os"
)
type WithIndelsSettings struct {
FastaFile string
OutFile string
BranchLength float64
PropIndels float64... |
89a5771ca62bc5f6c60d3f9530de83a5a32374ce470d2f039e04446b4812a8ca | Go | 3,655 | 107 | package main
import (
"bytes"
"github.com/vertgenlab/gonomics/exception"
"io"
"log"
"path/filepath"
"strings"
"sync"
"time"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/genomeGraph"
"github.com/vertgenlab/gonomics/giraf"
"github.com/vertge... |
697439883d495478619b1dc79e3d53d3e12db06e2f8a673208e53b7689d30a6c | Go | 3,663 | 99 | package gtf
import (
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/vcf"
)
// VariantArrayOverlap takes a vcf record and a map of bool slices (chrom name maps to a bool for each base in that chrom).
// The bool slice encodes the presense/absense of some genomic feature and true is return... |
aa161bdc1a800d607373974c44f841935389be4d2bfed5f209229c9262413cab | Go | 3,699 | 112 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var OverlapEnrichmentsTests = []struct {
Method string
Elements1File string
Elements2File string
SearchSpaceFile string
OutFile string
ExpectedFile s... |
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