sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
713ff3a12e1576afb8e7ee2318826c2c43e102540bb1c3c088036d8bc1908607 | Go | 863 | 28 | package interval
import (
"testing"
"github.com/vertgenlab/gonomics/bed"
)
func TestMergeIntervals(t *testing.T) {
var testIntervals []Interval = []Interval{
&bed.Bed{Chrom: "1", ChromStart: 1, ChromEnd: 8},
&bed.Bed{Chrom: "1", ChromStart: 3, ChromEnd: 5},
&bed.Bed{Chrom: "1", ChromStart: 4, ChromEnd: 4},
... |
43dd7c0b96ab696e1a7628e417c6f4691d191418ffa7b20e41c13c2fada83ff7 | Go | 865 | 34 | // Command Group: "General Tools"
// View http url links and print data stream to stdout
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/fileio"
)
func usage() {
fmt.Print(
"goFetchCat - view http url links and print data stream to stdout\n Usage:\n ./goFetchCat link.com/file.txt\n... |
9276c9eae2660d8df8a4188b5afed0141aa8943a4297692ecb6ecabffdbec017 | Go | 868 | 42 | package main
import (
"flag"
"fmt"
"log"
)
func usage() {
fmt.Printf(
"samInfo - a collection of tools for extracting information from SAM/BAM files." +
"Usage:\n" +
"\tsamInfo readLength in.sam/bam out.txt\n" +
"\tOR\n" +
"\tsamInfo coverage in.sam/bam histogram.txt statSummary.txt\n" +
"\tOR\n"... |
783ab72419bba379964ecd6ffbf7cf10e8a60d6833e625a7a964ebf0855c1845 | Go | 879 | 37 | package bed
import (
"io"
)
// Current methods satisfy requirements for the following interfaces:
// bed.BedLike
// GetChrom returns the chrom of the bed struct.
func (b Bed) GetChrom() string {
return b.Chrom
}
// GetChromStart returns the starting coordinates of the bed struct.
func (b Bed) GetChromStart() int ... |
b02e28db273d1346d123187398f2f31196234d6ce65c3414e8ad235b0e39aab2 | Go | 879 | 36 | package main
import (
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/vcf"
"os"
"testing"
)
var SampleVcfTests = []struct {
inputFile string
expectedOutputFile string
numVariants int
numSamples int
}{
{"testdata/babyTest.vcf", "testdata/babyTest_expec... |
da33616d47ea2451f0f16a1cc5040f196b89c5e00584a5ce9566ca80258accde | Go | 881 | 39 | package chain
import (
"io"
)
// GetChrom returns the name of the target chromosome
func (ch Chain) GetChrom() string {
return ch.TName
}
// GetChromStart returns the starting position on the target chromosome
func (ch Chain) GetChromStart() int {
if ch.TStrand {
return ch.TStart
} else {
return getSwapTCoor... |
f7c8767bfe000a18ca81690499e8e9078176113d38c7b8bec3727e6105657a6d | Go | 884 | 44 | // Command Group: "Sorting"
// Topologically sorts nodes in a genome graph (.gg) file
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/genomeGraph"
)
func usage() {
fmt.Print(
"sortGraph - Topologically sorts nodes in a genome graph (.gg) file. \n" +
"Usage:\n" +
" sortGraph inp... |
056f2eb5be92d2e66f40370c02d2af616ca6ccacf92a0e7cc4d623cd8e1bf028 | Go | 891 | 32 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var digestGenomeTests = []struct {
inFile string
outFile string
expectedFile string
motif string
}{
{"testdata/in.fa", "testdata/out.MboI.bed", "testdata/expected.MboI.b... |
6b3f205efd60027c6628e1a3dd792128a53a242996513805a08aae17010cd0c0 | Go | 892 | 45 | package lift
import (
"testing"
)
var TotalSizeTests = []struct {
filename string
expected int
}{
{"testdata/elements1.bed", 460},
{"testdata/elements2.bed", 6},
}
func TestTotalSize(t *testing.T) {
var b []Lift
var actual int
for _, v := range TotalSizeTests {
b = GoRead(v.filename)
actual = totalSize(b... |
3403932249821ac85724b6bd71a99b7c80dc31d7533a273970c2ff38aa03d702 | Go | 900 | 34 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var mafToMultiFaTests = []struct {
mafFile string
refFile string
speciesFile string
outMultiFaFileExpected string
noMask bool
}{
... |
10b9622fdebcff4641049445b5816d0ee8887b232f648aaa18700640dda8b5ea | Go | 901 | 34 | package numbers
import (
"math"
"testing"
)
var highestDensityIntervalTests = []struct {
Trace McmcTrace
Start float64
End float64
Mean float64
Proportion float64
}{
{McmcTrace{Parameter: []float64{0.1, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 20.0}}, 2.0, 9.0, 6.41, 0.8},
}
func TestHi... |
c363073dba8443dcc7bba2638545a3a897e899225cc077af77cec852c8c4ef5b | Go | 906 | 51 | package numbers
import (
"testing"
)
func TestIntToRoman(t *testing.T) {
testCases := []struct {
input int
expected string
}{
{1, "I"},
{3, "III"},
{4, "IV"},
{9, "IX"},
{58, "LVIII"},
{1994, "MCMXCIV"},
{3994, "MMMCMXCIV"},
}
for _, test := range testCases {
result := IntToRoman(test.inp... |
151338c9e616fa6bf1d12edacf3312f204e0796c23c9b9848f3f753f5671d784 | Go | 907 | 38 | package wig
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var ReadWholeGenomeTests = []struct {
InFile string
ChromSizeFile string
DefaultValue float64
OutFile string
ExpectedFile string
}{
{InFile: "testdata/wholeGenome.wig",
C... |
3a196f256922a54acbb414b0d72909eb160480c782a1882645bf26e3130c482e | Go | 909 | 31 | package fasta
import (
"strings"
"github.com/vertgenlab/gonomics/chromInfo"
)
// IsFasta returns true if the input filename has a fasta file extension.
// Input filename may have a .gz suffix.
func IsFasta(filename string) bool {
if strings.HasSuffix(filename, ".fasta") ||
strings.HasSuffix(filename, ".fa") ||
... |
928983e1a871969b36b85680b525ea4027e3f4191ed0c47a2d098aa484929643 | Go | 909 | 35 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var SimulateBedTests = []struct {
RegionCount int
SimLength int
MatchedBed string
NoGapFile string
OutFile string
SetSeed int64
ExpectedFile string
}{
{10, 1000, ""... |
99182543be6399a3bd23ba0b194f695c41b62875840bcde980352d638a2f2af7 | Go | 914 | 43 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/ontology/obo"
"log"
)
func oboToDot(oboFile string, term string, output string) {
oboRecords, _ := obo.Read(oboFile, false)
obo.SubtreeToDot(output, term, oboRecords)
}
func usage() {
fmt.Print(
"oboToDot takes in an obo file and the id bel... |
63734715140811bb7fc20f6f98d0231fdf6182ee675f282898d3edefc6e367a7 | Go | 915 | 34 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var DunnIndexTests = []struct {
InputBed string
InputFa string
InputGroup string
OutFile string
ExpectedFile string
Realign bool
}{
{"testdata/test.bed", "testdata... |
cdfbf49a224be32bd8eb4fe69bed2d694e566ca5a89dd1cb44bc9bdf777d012f | Go | 922 | 36 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"os"
"testing"
)
var RandSeqTests = []struct {
outFile string
expectedFile string
GC float64
numSeq int
lenSeq int
setSeed int64
}{
{"testdata/test.fa", "testdata/expected... |
0524e2b9d3b995f465d6a36c76a424ca5e2305e90c30fc81a320051fe5be8d67 | Go | 924 | 37 | package fileio
import (
"bufio"
"fmt"
"github.com/klauspost/pgzip"
"net/http"
"strings"
"github.com/vertgenlab/gonomics/exception"
)
// EasyHttp will fetch data from files uploaded to an internet server and stream data into EasyReader.
func EasyHttp(url string) *EasyReader {
answer := EasyReader{}
resp, err ... |
43d33d6554538fe879baa4f6ffd67087ba2a1861114a851c5e7447aa3cb99c33 | Go | 931 | 40 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var OboToolsMappingTests = []struct {
InFile string
OutFile string
Force bool
ExpectedFile string
}{
{InFile: "../../ontology/obo/testdata/test.obo",
OutFile: "te... |
7b7214f93f46581b0bbbcba0e1d43531592a8d4900a9449869935949b0b5acb2 | Go | 931 | 40 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var bedCountBamTests = []struct {
inBam string
inBed string
outFile string
expFile string
normalize bool
}{{
"testdata/in.sort.bam", "testdata/in.bed", "testdata/out.txt", "t... |
a4dc09457e01fb033ea8c68df4d3b7042d170c3b50d50fc8a8ad1a76df850f69 | Go | 936 | 35 | package gaf
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
func TestReadAndWrite(t *testing.T) {
var err error
actual, header := Read("testdata/test.gaf")
Write("testdata/out.gaf", actual, header)
if !fileio.AreEqual("testdata/out.gaf", "testdata/t... |
684c336889e133e87bbb47b126bc7e621c0d4aa322d91b932ef91e33077e4a34 | Go | 939 | 41 | package wig
import (
"github.com/vertgenlab/gonomics/exception"
"os"
"testing"
"github.com/vertgenlab/gonomics/fileio"
)
var SmoothTests = []struct {
InFile string
ChromSizes string
OutFile string
WindowSize int
Missing float64
ExpectedFile string
}{
{InFile: "testdata/unsmooth.wig",
... |
44ea70e2543b8f418e30893509448beee4fb7da540b0cdf42a02fba14f293c2e | Go | 944 | 31 | package bed
import (
"log"
"testing"
)
var r1 Bed = Bed{Chrom: "chr1", ChromStart: 1, ChromEnd: 2}
var r2 Bed = Bed{Chrom: "chr1", ChromStart: 4, ChromEnd: 5}
var r3 Bed = Bed{Chrom: "chr1", ChromStart: 10, ChromEnd: 11}
var r4 Bed = Bed{Chrom: "chr1", ChromStart: 12, ChromEnd: 14}
var querySlice []Bed = []Bed{r1,... |
3d4031fdafcba0cd26aa7af488a369d188a0b2b288e33e717e0b3105bfa2747d | Go | 946 | 32 | package simulate
import (
"math/rand"
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/sam"
)
func TestSam(t *testing.T) {
var err error
rand.Seed... |
dcaeba37b9115841b69a17ee6db60f340a3347ee737f8eb00cf7c36be5f91540 | Go | 946 | 26 | package genomeGraph
/*
import (
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/giraf"
"github.com/vertgenlab/gonomics/sam"
//"github.com/vertgenlab/gonomics/align"
"log"
"os"
"sync"
"testing"
"time"
)
//TODO: finish writing matrix helper fu... |
e104a7f91e8c38f0646b74e90f9adba5a2980f58156f54dcbf7a81181a78641f | Go | 946 | 42 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var FilterTests = []struct {
InFile string
ChromSizes string
OutFile string
ExpectedFile string
Chrom string
}{
{InFile: "testdata/filter/in.filter.wig",
ChromSizes... |
a008cf975ad7f9baf3a71f49c7816b85e081d3ea368588364ecb613b7a051489 | Go | 966 | 51 | package numbers
import (
"log"
"golang.org/x/exp/constraints"
)
// Max returns the maximum of two input values of an ordered type.
func Max[E constraints.Ordered](a, b E) E {
if a > b {
return a
}
return b
}
// Min returns the minimum of two input values of an ordered type.
func Min[E constraints.Ordered](a,... |
1d1eb970d6da6aec1d4b224be25756cbca991392d4c6432c90e5e8d3b363dd18 | Go | 971 | 40 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var ScCountTests = []struct {
InFile string
OutFile string
ExpectedFile string
GeneFile string
ExpNormalizationFile string
}{
{"testdata/t... |
b7fda60d23f82634d218fcc7168b1aba32862b8a8f7e02ca535abbc907ef81ee | Go | 973 | 40 | package bedpe
import (
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
)
func AllAreEqual(a []BedPe, b []BedPe) bool {
if len(a) != len(b) {
return false
}
for i := range a {
if !Equal(a[i], b[i]) {
return false
}
}
return true
}
... |
ffeb993fdce169e3c809dc89fc6c4c409713ef39fce3cae0d2dfb89e937ac509 | Go | 977 | 33 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var BedMinimumDistanceNameTests = []struct {
inputBed string
genomeBed string
outputBed string
expectedBed string
}{
{"testdata/inputBed1.bed", "testdata/genomeBed1.bed", "testdat... |
63fdffc1e240399df3856af561bcfe819f65f457b092280caa84e58bcd91e5d2 | Go | 992 | 36 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var geneIdToNameTests = []struct {
geneNameTable string
in string
out string
ncbi bool
ensembl bool
keepMatching bool
expectedFile string
}{
{"te... |
08988d034fd6a969db24bbbf03663d99206b2d810e912581f11e8c1a8c390cf0 | Go | 994 | 49 | // Command Group: "Motif Tools"
// A collection of tools for manipulating position matrices
package main
import (
"flag"
"fmt"
"log"
)
func usage() {
fmt.Printf(
"pwmTools - a collection of tools for manipulating position matrices.\n" +
"Usage:\n" +
"\tpwmTools filter in.pwm out.pwm\n" +
"\tOR\n" +
... |
9f0ae48808c986ef283ab1a60bd66364b493e3cfc3b368fd0852c304192228b2 | Go | 1,003 | 44 | // Command Group: "Sequence Evolution & Reconstruction"
// Generates a newick tree file from an input dot format tree
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/tree"
"log"
)
func dotToNewick(inFile string, outFile string, verbose bool) {
t := tree.ParseDot(inFile, verbose)
tree.WriteNe... |
7b6214dce814c05ec483cca11f913b7f1866e368f9f494154ca148a3cd7134e5 | Go | 1,012 | 56 | package giraf
import (
"strings"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
)
func isEqual(a *Giraf, b *Giraf) bool {
if strings.Compare(a.QName, b.QName) != 0 {
return false
}
if a.QStart != b.QStart {
return false
}
if a.QEnd != b.QEnd {
return false
}
if a.PosStran... |
75c8e9369339899dd8c55ffb70d83783d65b12d57eac527748bbe00e542c320c | Go | 1,016 | 47 | package fit
import "testing"
var LagrangeInterpolationTests = []struct {
queryX float64
dataPoints [][]float64
expectedY float64
}{
{ //first parabola is y=x^2 + 1
queryX: 0.5,
dataPoints: [][]float64{
{1.0, 2.0},
{2.0, 5.0},
{3.0, 10.0},
},
expectedY: 1.25,
},
{ // next is linear interpol... |
83d1af2c6e78cf9667b477f0b42524f9a58bc0e0fd367d778d3446e2206d9209 | Go | 1,025 | 56 | package convert
import (
"strings"
"testing"
)
var ChromNameTests = []struct {
Ucsc string
Ensembl string
}{
{"chr1", "1"},
{"chr2", "2"},
{"chr3", "3"},
{"chr4", "4"},
{"chr5", "5"},
{"chr6", "6"},
{"chr7", "7"},
{"chr8", "8"},
{"chr9", "9"},
{"chr10", "10"},
{"chr11", "11"},
{"chr12", "12"},
{"c... |
d1d3818fb1ab3c1d51dcf0cda444837a82890fbb6610de427d563ed2a523a6f6 | Go | 1,025 | 49 | package fasta
import (
"testing"
"github.com/vertgenlab/gonomics/chromInfo"
)
func TestIsFasta(t *testing.T) {
if !IsFasta("test.fa") {
t.Errorf("Problem is IsFasta")
}
if !IsFasta("test.fa.gz") {
t.Errorf("Problem is IsFasta")
}
if !IsFasta("test.fasta") {
t.Errorf("Problem is IsFasta")
}
if !IsFasta... |
ac2e957fa92eea0f225194d167fea343f2d3c0b4c3eab969df879212804de352 | Go | 1,036 | 39 | package sam
import (
"testing"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
)
func TestEqual(t *testing.T) {
if !Equal(r001, r001) || // find tested records in io_test.go
Equal(r001, r002) ||
Equal(r001, r001Supplemental) ||
Equal(r003, r002) ||
!Equal(r002, r002) ||
Equa... |
12add1ae0f4fe0a48f8bff9e492e7ed99785f184d8de7e6109d077c7f6f09901 | Go | 1,053 | 46 | // Command Group: "Sequence Evolution & Reconstruction"
// Simulate sequence evolution on an input fasta from the root of a newick tree to the leaf nodes
package main
import (
"flag"
"fmt"
"log"
)
func usage() {
fmt.Print(
"simulateEvol - a suite of tools for molecular evolution simulation.\n" +
"Select a s... |
bd0ebc1ed5c7fc6fea2c1218d008185673093a8cf9cefa8e87a2c33243798155 | Go | 1,053 | 30 | package sam
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
)
var singleCellTests = []struct {
InFile string
ExpectedBx []string
ExpectedUmi []string
}{
{"testdata/singleCell.sam", []string{"AGTGCACGTGGAGGCT", "AGTGCACGTGGAGGCT", "AGTGCACGTGGAGGCT", "GGACAGTTAGACAAGT", "GCTAGGACAATGAGTA", "CAGGAC... |
47552aec51a0e947c56f8d4a3ee4184b11f6127bf8612f55a86d6154a807f058 | Go | 1,067 | 28 | package dnaThreeBit
import (
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/numbers"
)
// NewThreeBitRainbow builds a "rainbow table" of a sequence in ThreeBit format
// with every possible offset, so that there is always a version of the sequence
// that can be compared to another ThreeBit se... |
878b9c29d7a3268ef6edd28252ddb1086f5355795068cce19a9d0d082ddaca8e | Go | 1,085 | 44 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var BedGcContentTests = []struct {
BedFile string
FaFile string
OutFile string
ExpectedFile string
MultiFaMode bool
Species string
}{
{BedFile: "testdata/test.bed... |
8e8f6d62a593f47c83ebfb808d1865d0d2d46342199508d6f0a78a00df26bd06 | Go | 1,087 | 45 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var WigStatsTests = []struct {
InputNoGapBed string
ChromSizes string
InputWig string
OutputFile string
ExpectedFile string
MissingDataValue float64
}{
{Input... |
cd37f791d34ddc94b2188850bce628b2491d3dfbecd7e8d753efe5854a1a1635 | Go | 1,100 | 42 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var BedMathTests = []struct {
Afile string
Bfile string
Outfile string
ExpectedFile string
Op string
}{
{"testdata/testA.bed", "testdata/testB.bed", "testda... |
bf4b8463e64bb7ad5f5cf2a2d566d33b16a9834d24fc7f5e6cfbdf05423c6a68 | Go | 1,101 | 35 | package numbers
import (
"fmt"
"github.com/vertgenlab/gonomics/fileio"
)
// Plot returns the values of a function(float64) float64 between a left and right bound for a specified number of bins.
// the answer is written to a file as a CSV for subsequent visualization.
// Half-closed interval [left, right).
func Plo... |
0f8b6c5251b8d9e5987f4b8222e19825c7351cbb387738514faa61d3b7ccf3fa | Go | 1,110 | 38 | package align
import (
"testing"
"github.com/vertgenlab/gonomics/fasta"
)
var multiAlignTests = []struct {
input string
expected string
}{
{"testdata/multiAlignTest.in.fa", "testdata/multiAlignTest.expected.fa"},
{"testdata/multiAlignTest.in2.fa", "testdata/multiAlignTest.expected2.fa"},
}
func TestMultiAl... |
d2806b50bf81ba706c851ad73e08fb9c88978f4470a087f29b1d00f21cec4041 | Go | 1,110 | 49 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var BedShearTests = []struct {
InFile string
OutFile string
ExpectedFile string
FragmentSize int
}{
{InFile: "testdata/test.bed",
OutFile: "testdata/tmp.1.bed",
Expect... |
87946d98884a2e48e6e44333902e9e234bbed663cd30c5b5b7236a6b0020b5ae | Go | 1,113 | 37 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var MaqqTests = []struct {
infile string
outhistogram string
bedregions string
expected string
}{
{infile: "testdata/mapq/test1.sam", outhistogram: "testdata/mapq/out.hist.txt... |
4ebf941ae90f48da3310975392997e37210e7037b39f184a7930da15aa6af660 | Go | 1,117 | 50 | package pFasta
import (
"github.com/vertgenlab/gonomics/fileio"
"math/rand"
"testing"
)
var RandSeqTests = []struct {
Length int
Name string
SeedSet bool
SetSeed int64
RandSource *rand.Rand
Expected string
OutFile string
Precision float32
}{
{Length: 5,
Name: "chr1",
SeedSe... |
030e23973c03bb982eaae4c2e731febf292bcb022166ad004d487c0a14e3d5cd | Go | 1,134 | 53 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var FaToPredictSetTests = []struct {
InFile string
OutFile string
ExpectedFile string
WindowSize int
Stride int
WithRevComp bool
}{
{InFile: "testdata/test.fa",
O... |
c62555906af4dae084bd1a8edab69614477b8fcd247f7dd4870bbb87c1eb3630 | Go | 1,137 | 24 | package genomeGraph
//"github.com/vertgenlab/gonomics/dna"
//"github.com/vertgenlab/gonomics/fastq"
//"log"
//"testing"
//TODO: consider dot format to graph
// --> node_1 --> node_4
//node_0 --> node_3 --> node_6
// --> node_2 --> node_5
//TODO: The function this te... |
c41cea3250e4c38a43bb0deab5ac5d2502c848c1d101401ba8335a31d96f7028 | Go | 1,139 | 53 | // Command Group: "FASTA and Multi-FASTA Tools"
// Filter a maf file to remove entries below a score threshold
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/maf"
)
func mafFilter(inFile string, outFile string, threshold float64) {
mafRecords := maf.Read(inFile)
var outMaf []*maf.Maf... |
fc4fc162b62d38b54ec51d42874a2cafaee7268d669ff2aab43325ae75867773 | Go | 1,141 | 27 | package genomeGraph
import (
"sync"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/sam"
)
// this is just for speed testing to see how much of the speed slowdown is due to alignment time.
func gswNothingWorker(gg *GenomeGraph, seedHash map[uint64][]u... |
37b75e40057861d3c7560e4d2bddf4d52b76ed339420812a7e36b37678737f1d | Go | 1,142 | 38 | package align
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
)
var alignTests = []struct {
seqOne string
seqTwo string
aln string
}{
{"ACGT", "ACGT", "ACGT\nACGT\n"},
{"ACGT", "CGT", "ACGT\n-CGT\n"},
{"ACGT", "ACG", "ACGT\nACG-\n"},
{"CGT", "ACGT", "-CGT\nACGT\n"},
{"ACG", "ACGT", "ACG-\nACGT\n... |
ca9126e955c458cea005e06335ff93c1222a11699bc92ec36141db272c5d0da5 | Go | 1,149 | 58 | package gtf
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/vcf"
)
func TestVcfToVariant(t *testing.T) {
var inVcf vcf.Vcf
var inGtf map[string]*Gene = make(map[string]*Gene)
var inSeq map[string][]dna.Base = make(map[string][]dna.Base)
inVcf.Chr = "DummyChr"
inVcf.Re... |
a59b8f8e081979fd4dd8b6043311e05bff6affd40c2fb1952963c0dfca3d40d2 | Go | 1,156 | 49 | package pFasta
import (
"github.com/vertgenlab/gonomics/fileio"
"testing"
)
var vcfToPfaTests = []struct {
InputVcf string
RefFa string
Start int
End int
Expected string
Output string
Precision float32
}{
{InputVcf: "testdata/test_vcfToPfa_input_1.vcf",
RefFa: "testdata/test_vcfToPf... |
2edc0220f0be5d1067d9723ccd2d4f9f90f52b21f719cd2a8ef5a1c5524dc031 | Go | 1,157 | 30 | package fit
import "log"
// LagrangeInterpolation returns f(queryX) for a given queryX. The function f(x) is
// estimated by Lagrange Interpolation using a set of input dataPoints in [][]float64 format,
// each data point is a []float64 with two elements, the first value is the x value and the
// second value is the ... |
19dfb418233d45d6bfdf529e04eaae183b6489cab314de1d1f52417307144e45 | Go | 1,158 | 70 | package psl
import (
"golang.org/x/exp/slices"
)
// Equal will check two psl structs and compare every single field of data to determine if they are the same.
func Equal(x, y Psl) bool {
if x.Match != y.Match {
return false
}
if x.MisMatch != y.MisMatch {
return false
}
if x.RepeatMatch != y.RepeatMatch {
... |
528d78c23f4c7fc614fdd3842a3161f7f384ecb22059dc92650153d2446d0f0f | Go | 1,168 | 55 | package vcf
import (
"bytes"
"testing"
)
func TestWriteVcf(t *testing.T) {
// Create a Vcf struct for testing
record := Vcf{
Chr: "1",
Pos: 1234567,
Id: "rs123456",
Ref: "A",
Alt: []string{"G", "T"},
Qual: 99.0,
Filter: "PASS",
Info: "DP=100",
Format: []string{"GT", ... |
a38db2244b0b277223b5e248e154adf27373a50c2dd1b962345b8fb4d5ccef5a | Go | 1,169 | 47 | package main
import (
"io/ioutil"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/giraf"
)
func TestGirafSort(t *testing.T) {
graphFile := "../../sort/testdata/mini.gg"
readsFile := "../../sort/testdata/miniReads.giraf"
outFile, err... |
950b52b7cfa15717b2ffe992e2a3437b6bb476ebffb961b36d777a0170bfc68c | Go | 1,170 | 52 | // Command Group: "WIG Tools"
// a collection of tools for manipulating Wig files.
package main
import (
"flag"
"fmt"
"log"
)
func usage() {
fmt.Printf(
"wigTools - a collection of tools for manipulating Wig files.\n" +
"Usage:\n" +
"\twigTools peaks in.wig chrom.sizes out.bed\n" +
"\twigTools filter ... |
cd53c85b10016d04f47108943d708d1a022689c96773f5dd12cefb6b50488eb3 | Go | 1,177 | 48 | package psl
import (
"testing"
)
var psldata Psl = Psl{
Match: 261,
MisMatch: 54,
RepeatMatch: 23,
Ns: 0,
QNumIns: 1,
QBaseIns: 1,
TNumIns: 0,
TBaseIns: 0,
Strand: "+-",
QName: "NM_001001576",
QSize: 376,
QStart: 2,
QEnd: 345,
TName: "c... |
364ac14a87ae46dae9af493ff94ee0c8251bd94fd1d90189f6f8a17fc4c7ad16 | Go | 1,179 | 45 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/wig"
"os"
"testing"
)
var entropyTrackTests = []struct {
InFile string
OutFile string
ChromSizes string
ExpectedFile string
DefaultValue float64
}{
{InFile: "testdata/test_sample_input.pfa",
OutFi... |
5b9586d03c7ba3cfe739de7f90ea0268cafc99ab1ffbc226ae08362622986d79 | Go | 1,189 | 45 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var FastqReplaceSeqTests = []struct {
inFile string
outFile string
expectedFile string
findReplaceFile string
findReplaceDelim string
ignoreCase ... |
d6d8a4e703449d936e75cf83adbe76eadba712f9b7ea22ec2afe61d4403ce066 | Go | 1,192 | 28 | package sam
import (
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"testing"
)
func TestSamBedToBases(t *testing.T) {
var obs []dna.Base
rec := []Sam{
{RName: "chrA", Pos: 101, Cigar: cigar.FromString("10M"), Seq: dna.StringToBases("AACCTTGGAA... |
03d5aaa2c02e470bc768408c68888895a1fe9994f60e34e16549f17627d7d935 | Go | 1,199 | 72 | package sam
import (
"bytes"
"errors"
"fmt"
"io"
"io/ioutil"
"os"
"strings"
"testing"
)
func TestBamWriter(t *testing.T) {
var err error
err = testFile("testdata/small.sam")
if err != nil {
t.Error(err)
}
}
func TestBamWriterAuxTags(t *testing.T) {
var err error
err = testFile("testdata/auxTagTest.sa... |
e44ae798214f0bfaea67b5557ee5087b746acb66b2b5ba229316e62c058330e4 | Go | 1,203 | 43 | package bed
import (
"os"
"testing"
)
var b1 Bed = Bed{Chrom: "chr1", ChromStart: 100, ChromEnd: 200, Name: "First", Score: 1, Strand: '+', FieldsInitialized: 6}
var b2 Bed = Bed{Chrom: "chr2", ChromStart: 400, ChromEnd: 900, Name: "Second", Score: 5, Strand: '-', FieldsInitialized: 6}
var b3 Bed = Bed{Chrom: "chr3... |
e065924d60c74189da620978890957e2a396cffd76f8e612deceebfcd48cd08c | Go | 1,215 | 46 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
func TestSimPcr(t *testing.T) {
template := "testdata/test.fasta"
primers := []string{
"GCCTCCGTGAGGCTAC",
"TTGAGGATCTTTTCTTCACG",
}
simulatePcr(primers, template, "testdata/actual1.b... |
ddd5a6ddcd5ef163bfece1429b40c48a7262e32bff03c5e7787f268136e1e90d | Go | 1,219 | 37 | package vcf
import (
"strings"
"testing"
)
var IG1 Sample = Sample{[]int16{1, 0}, []bool{false, false}, []string{""}}
var IG2 Sample = Sample{[]int16{0, 0}, []bool{false, false}, []string{""}}
var IG3 Sample = Sample{[]int16{1, 1}, []bool{false, false}, []string{""}}
var EG1 Sample = Sample{[]int16{0, 1}, []bool{f... |
69e64d8697697d92dff6b8c6aa25e6124cb82e9a52cb6e9a2f8b22a605ffdc43 | Go | 1,220 | 45 | package tree
import (
"image/png"
"os"
"testing"
)
var treeDrawTests = []struct {
treeText string
tmpFilename string
}{
{"(human,chimp)ancestor;", "testdata/tmp.1.png"},
{"((human,chimp)humanChimpAncestor,rhesus);", "testdata/tmp.2.png"},
{"(((human,chimp),(mouse,rat)),dog);", "testdata/tmp.3.png"},
{"((p... |
3feb803109fb41f4623eec6055ed41d051750f5f1acaba2cb7674225d9abd0ed | Go | 1,229 | 42 | package vcf
import (
"log"
//DEBUG: "fmt".
)
// invertSample inverts the ancestral/derived state for each allele in a Sample. Only works for biallelic positions, throws an error if an allele state is greater than 1.
// TODO: this is currently only supported for biallelic bases.
func invertSample(g Sample) Sample {
... |
0c900021a0e68ba0e7e200e33cc2d5791817fd261c44afd89de57a2ff02b9a9c | Go | 1,234 | 51 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/sam"
"testing"
)
func TestTagToReadGroup(t *testing.T) {
in := "testdata/tagTest.bam"
valueFile := "testdata/tagTestValues.txt"
targetTag := "CB"
out := "testdata/testOutput.bam"
bamTagToReadGroup(in, out, target... |
a79622c7e7f738e21bed6c5342966dcc015901810974199a972081d528ccc5b0 | Go | 1,235 | 32 | package browser
import (
"testing"
"github.com/vertgenlab/gonomics/fileio"
)
var multiFaVisualizerTests = []struct {
inFile string
outFile string
start int
end int
noMask bool
lineLength int
expectedFile string
endOfAlignment bool
}{ //here the infile is the... |
90a901e2823d1d04dd32ad9a74cc7738ee7752877da14d27f6a64e6388067a30 | Go | 1,240 | 40 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
//note that the discrete functions are plotted in main, so these are tested in
//the popgen package.
var PlotFunctionsTests = []struct {
Function string
FunctionArgs string
Left ... |
c200a3e5bd849b8a6cfca291cf0ce20f5efbadd454ce04cda018e2039998dc6a | Go | 1,247 | 42 | package dnaTwoBit
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
)
var dnaStrings = []string{
"TCATACGTTTTTTTTTTTTTCTGTC",
"TCAAAACCCCCGGGGTTTTTCTGTC",
"TCATACGTACGTACGTCCCCCTGCCCC",
"TCATGGGGGGGGCCAGTACGTTGGCT",
}
func TestDnaToFromString(t *testing.T) {
var singleBase dna.Base
for _, input := ran... |
8fa5605ebcc9b12f92d84247f9008f19657e69cd0ca4eb7c9f766d3c09131a27 | Go | 1,259 | 45 | package axt
import (
"fmt"
"testing"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/sam"
)
func TestSamFileConvert(t *testing.T) {
//chr19 3001012 3001075 chr11 70568380 70568443 - 3500
var testAxt = Axt{
RName: "chr19",
RStart: 1,
RE... |
64121b45d3292569634ccadad71ff0fae4b8c996ed7caf656c525c0696228b59 | Go | 1,260 | 37 | package main
import (
"os"
"path/filepath"
"strings"
"testing"
"github.com/vertgenlab/gonomics/exception"
)
func TestGonomics(t *testing.T) {
// check to see if binary is already installed, if so buildCmdCache, else return
// Find binary location. Preference is gonomics exec path > GOBIN > GOPATH > Default g... |
9f9bd9d803e062968b1b27852d669fc4c7b08dadf11628ffcd7d09d772313eae | Go | 1,263 | 48 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var LocateCGTest = []struct {
inFa string
chromName string
outfile string
compare bool
cgtype string
expectedTxt string
}{
{"testdata/single_genome_test.fa", "chr... |
9e2db55b5017dfcc473836bd7dd8518dc4a131d0f6c8e5731f957fa9f1b76ac2 | Go | 1,270 | 52 | package main
import (
"github.com/vertgenlab/gonomics/fasta/pFasta"
"github.com/vertgenlab/gonomics/fileio"
"testing"
)
var IlsReconstructTests = []struct {
PostProbsFiles string
ReconFiles string
ChromSizesFile string
OutDir string
Precision float32
Expected string
TestPrecision flo... |
d095d191d6fbb61739dd9238277d3abaf32f1577e54df77251035287da60fea6 | Go | 1,276 | 31 | package genomeGraph
import (
"log"
"testing"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
)
//func RightLocal(alpha []dna.Base, beta []dna.Base, scores [][]int64, gapPen int64, m [][]int64, trace [][]rune) (int64, []*cigar.Cigar, int64, int64, int64, int64)
func TestRightLocal(t *... |
b03e4e9e8f51335332b57fb49e97aab94d381ccd47fd30784a733ec796e2fa25 | Go | 1,277 | 55 | package variant
import (
"github.com/vertgenlab/gonomics/dna"
)
// Substitution describes a single base change.
// Pos is the 0-base position of the changed base.
// (e.g. ATG sub 1 T>C -> ACG).
type Substitution struct {
Chr string
Pos int
Ref dna.Base
Alt dna.Base
}
// Insertion describes an insertion into a ... |
08f9955da0f3ab4ec93704f79a18045dc6a665f90152a93dff2b02b5937f20f3 | Go | 1,291 | 63 | package bed
import "testing"
var TotalSizeTests = []struct {
filename string
expected int
}{
{"testdata/elements1.bed", 460},
{"testdata/elements2.bed", 6},
}
func TestTotalSize(t *testing.T) {
var b []Bed
var actual int
for _, v := range TotalSizeTests {
b = Read(v.filename)
actual = TotalSize(b)
if ac... |
7e8373f78cc7b0ca3635dc14d5645ea8cb80dfd8a068bcca19074e2c35eeb4df | Go | 1,291 | 51 | package sam
import (
"log"
"strings"
"github.com/vertgenlab/gonomics/dna"
)
// SingleCellAlignment includes a Sam struct along with the parsed barcode and UMI for single-cell reads.
type SingleCellAlignment struct {
Aln Sam
Bx []dna.Base
Umi []dna.Base
}
// ToSingleCellAlignment parses the barcode and UMI fr... |
c39a31eeb548ae32ca51ab7a09ee161e1c5d5b3f984f8557f768e4f2fdda02d5 | Go | 1,297 | 76 | package dna
import (
"fmt"
)
func ExampleStringToBases() {
var stringSeq string
stringSeq = "ACGT"
fmt.Println(stringSeq)
var baseSeq []Base
baseSeq = StringToBases(stringSeq)
fmt.Println(baseSeq)
// Output:
// ACGT
// [0 1 2 3]
}
func ExampleBasesToString() {
var baseSeq []Base
baseSeq = []Base{A, C, G... |
c3b4141bf4ff975bc138b292ba7d4b0f502c1d808ba2d0baa4b130a345010ef1 | Go | 1,297 | 47 | package main
import (
"fmt"
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var SlurmGeneralizedCheckTests = []struct {
inputFancyFile string
actualOutputParseTheInput string
expectedOutputParseTheInput string
}{
{"testdata/inputFancyFile.tx... |
331e708d928e7f828dd8781110297e5d205dfec23a1e3de7000ed390d06a39ed | Go | 1,298 | 50 | package bedpe
import (
"testing"
"github.com/vertgenlab/gonomics/bed"
)
var Equal1 BedPe = BedPe{A: bed.Bed{Chrom: "chr9", ChromStart: 60, ChromEnd: 75}, B: bed.Bed{Chrom: "chr9", ChromStart: 7500, ChromEnd: 7900}}
var Equal2 BedPe = BedPe{A: bed.Bed{Chrom: "chr12", ChromStart: 86500, ChromEnd: 86540}, B: bed.Bed{... |
b98d58aaa2b865fa756da63dea10b048a1c9300fcf3d0a47fa19b7c7b92c5992 | Go | 1,298 | 62 | package vcf
import (
"testing"
)
func TestSnp(t *testing.T) {
tests := []struct {
vcf Vcf
expected bool
}{
{Vcf{Info: "SVTYPE=SNP"}, true},
{Vcf{Info: "SVTYPE=INS"}, false},
{Vcf{Info: "SVTYPE=DEL"}, false},
{Vcf{Info: "SOMEOTHERINFO;SVTYPE=SNP;MOREINFO"}, true},
}
for _, test := range tests {
... |
1115c76943a7957f4ef091153552c4c4157419115d26c1c3c17a87089f9d9c9f | Go | 1,299 | 56 | package main
import (
"github.com/vertgenlab/gonomics/fasta/pFasta"
"github.com/vertgenlab/gonomics/fileio"
"testing"
)
var vcfToPfaTests = []struct {
InFile string
RefFile string
OutDir string
Start int
End int
Expected string
Precision float32
}{
{InFile: "testdata/test_vcfToPfa_input_1.vcf",
RefFile:... |
50dd79b6b457be37d9c9dd2e7420eee92c464873c2a8ceb96b3e612188015303 | Go | 1,309 | 47 | package numbers
import (
"fmt"
"testing"
)
var RandBinomialTests = []struct {
N int
P float64
VariateCount int
ExpectedProb []float64
ExpectedAlias []int
}{
{N: 5,
P: 0.1,
VariateCount: 20,
ExpectedProb: []float64{1, 0.9683600000000008, 0.4374000000000003, 0.04860... |
c29c643b5e0f872ec1cd72f092441108c72c51b73d941538fa4addcc450ce47c | Go | 1,315 | 41 | package giraf
// flagTestBit test a single bit in a 16 bit flag.
func flagTestBit(num uint8, bit uint8) bool {
return bit&num == 0
}
// ProperlyAligned returns true if the aligner determined this read was aligned correctly.
func ProperlyAligned(giraf *Giraf) bool {
return flagTestBit(giraf.Flag, 1) // 2 in sam
}
/... |
59d7c6ddc9d6d839908e435d5d5597ce4cc4d65779c85270be5d0e7dbe1a534f | Go | 1,321 | 62 | package wig
import (
"fmt"
"testing"
)
var PearsonTests = []struct {
alpha map[string]Wig
beta map[string]Wig
missing float64
samplingFrequency float64
expected float64
}{
{
alpha: map[string]Wig{
"chr1": {
StepType: "fixedStep",
Chrom: "chr1",
S... |
40b8aa6cfd788405093bedd85c2cf440349e4fa1ae2308f52350e2163deacca2 | Go | 1,329 | 65 | package genomeGraph
import (
"sort"
"github.com/vertgenlab/gonomics/dna"
)
func compareId(alpha *Node, beta *Node) int {
if alpha.Id < beta.Id {
return 1
} else if beta.Id < alpha.Id {
return -1
} else {
return 0
}
}
func compareSeq(alpha *Node, beta *Node) int {
return dna.CompareSeqsCaseSensitive(alp... |
1fb06781b5f2cbeb17e0bb02090d3b531d627a0b086f0294fba7a21d576654e0 | Go | 1,331 | 46 | package numbers
/*
This file contains an implementation of an algorithm described in pseudocode in the following academic publication.
Generating Beta Variates with Nonintegral Shape Parameters.
R. C. H. Cheng
Communications of the ACM, April 1978.
*/
import (
"log"
"math"
"math/rand"
)
const RelError float64... |
7372b807783f6c48c68684587a27e2e6c3873e9f49b66b87d424da892a84d43c | Go | 1,346 | 37 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
var MultFaVisualizeBedsTests = []struct {
BedFile string
MultiFaFile string
OutFormat bool
NoMask bool
LineLength int
OutFiles []string
ExpectedFiles []strin... |
62fd9f4c774368b36928d85c3bc5b114372d50afc5ac7ca3fbc10fa96ac0b092 | Go | 1,363 | 40 | package dnaThreeBit
// Append adds "b" to the end of "fragment."
// "fragment" can be nil.
func Append(fragment *ThreeBit, b ThreeBitBase) *ThreeBit { // too confusing to have Append and append (from std lib) in this package?
var bNum uint64 = uint64(b)
if fragment == nil {
return &ThreeBit{Seq: []uint64{bNum << 6... |
72043deb28cdbf6e57e85813b15eacc4a78b7a22feff150efd87f9fe288dc12d | Go | 1,370 | 52 | package main
import (
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
"github.com/vertgenlab/gonomics/exception"
)
var MfaCountTests = []struct {
inputFile string
outputFile string
queryName string
both bool
either bool
secondQueryName string
thirdQueryName str... |
f72d870a39eb22006089a41e20248ba6d585d82bc38280301bd00edd8a75aafe | Go | 1,374 | 44 | package main
import (
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
// use struct to specify testdata.
var mafIndelsTests = []struct {
inMaf string
speciesIns string
speciesDel string
threshold float64
outInsBed... |
b5cf16dd4d80f5b039e45dee2dba2aa01c2908da994db6f445e1a054c108b6be | Go | 1,377 | 54 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"os"
"testing"
)
var tfMatchTests = []struct {
InFile string
MatrixFile string
OutFile string
MatrixFileType string
PropMatch float64
Pseudocounts float6... |
cb60835c891ade77bebe4b01b373e31f4931c3fb829d07713b1513da94f9a8ad | Go | 1,378 | 47 | package giraf
import (
"fmt"
"log"
"testing"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fileio"
)
// TODO: Will write a better high throughput test when random generator is working.
func TestReadAndWrite(t *testing.T) {
var numGiraf int = 1
gir... |
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