sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6ed83957fb8c8fef5efa6c237749deb2537d3d4a25aee766190b1565134412ed | Go | 7,921 | 190 | // Command Group: "FASTA and Multi-FASTA Tools"
// Returns a filtered fasta based on option parameters
package main
import (
"flag"
"fmt"
"log"
"path"
"strings"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
)
type settings struct {
InFile string
OutFile string
... |
4ab7918a58d3a0b665a494833f170a63c523effa2e9d576bcc448f1a51d2e105 | Go | 7,926 | 264 | package pFasta
import (
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/dna/pDna"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/vcf"
"log"
"math/rand"
"strings"
)
// checks if input pFasta has a sequence with chrom as name and returns its index
func checkIfChromInP... |
2c2e4c909881cc6449baa04f2c5da2dfaf0202c9a96c684bb3d2cb90de01c0d0 | Go | 8,037 | 256 | // Command Group: "Variant Calling & Annotation"
// Annotate a vcf file by querying various databases via CellBase
package main
import (
"bytes"
"encoding/json"
"errors"
"flag"
"fmt"
"io"
"log"
"net/http"
"os"
"strings"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"... |
381e696e7f586b44d4a85d5dbae9f9319e51c6fb294de78920818e5262a18ac3 | Go | 8,159 | 182 | // Command Group: "Sequence Evolution & Reconstruction"
// Reconstruct ancient sequences using extant genomes and a newick tree with branch lengths
package main
import (
"flag"
"fmt"
"log"
"strings"
"github.com/vertgenlab/gonomics/dna/pDna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gon... |
c28a6e361c943578cba1873d14ee869eb501eb1baad1d853cd0788034629de5c | Go | 8,160 | 259 | package bed
import (
"errors"
"log"
"sort"
"strings"
"github.com/vertgenlab/gonomics/numbers"
)
// SortByCoord sorts in place a slice of Bed structs by their genomic position.
func SortByCoord(bedFile []Bed) {
sort.Slice(bedFile, func(i, j int) bool { return Compare(bedFile[i], bedFile[j]) == -1 })
}
// SortB... |
ad882d15112e6dd332e7a0ccee3e97f757cc9a8abddd0aa9b46ea5dae147a43a | Go | 8,203 | 201 | // Command Group: "VCF Tools"
// Use the variant data in the vcf to edit an input fasta of the reference
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/vcf"
)
// addAnotherCopyOfRef takes an alignment and a n... |
6fbbe131c6759d273cfda4de4317f8bb2d167aa0b7c90f04d1d618866da43c6c | Go | 8,435 | 280 | package binaryGiraf
import (
"bytes"
"encoding/binary"
"io"
"log"
"math"
"github.com/vertgenlab/gonomics/bgzf"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/dna/dnaThreeBit"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonom... |
784a92efae9c937fb3c3d54bd2dba9315e39ad3d20f03376d9405a2dc868e3a0 | Go | 8,445 | 264 | package bigWig
import (
"testing"
)
var readHeaderTests = []struct {
InFile string
ExpectedBbiHeader BbiHeader
ExpectedZoomHeaders []ZoomHeader
ExpectedTotalSummary TotalSummaryBlock
ExpectedChromTreeHeader ChromTreeHeader
ExpectedChromTreeNodes []ChromTreeNode
}{
{InFile: "test... |
b3769ec727468c8bca6322bf5d21c47ebe216e1e045d7ac3e6eead9e9fc2a146 | Go | 8,480 | 236 | package main
import (
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fasta/pFasta"
"github.com/vertgenlab/gonomics/fileio"
"testing"
)
var ReconstructSeqTests = []struct {
NewickFile string
FastaFile string
OutFile ... |
414b28eff4242e07b48dc5c6ae1cbfd08ff959731fc746862e83fe7742f55bb0 | Go | 8,490 | 218 | // Package wig provides functions to read, write, and manipulate wig files.
// more information on the WIG file format can be found at https://genome.ucsc.edu/goldenPath/help/wiggle.html
package wig
import (
"errors"
"fmt"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/exception"
"gith... |
a502dbf9a3d6839da65a2643980cd1eedc2ad6090864cd86e6c73781fb7be54f | Go | 8,494 | 201 | // Package gene contains structs and functions to help understand protein-coding genes.
package gene
import (
"errors"
"github.com/vertgenlab/gonomics/dna"
)
type Feature int32
type MutationType byte
const (
Intron Feature = -1
UtrThree Feature = -3
UtrFive Feature = -5
// All positive values refer to cDN... |
4f9e5753e7dc7b6c0212c8fb2ac6db73b4b602fae49bfab70c83a921eee0e080 | Go | 8,677 | 228 | package lift
import (
"log"
"math"
"strings"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/logspace"
)
// ElementOverlapProbabilities returns a slice of float64 representing the probabilities that an element in elements2 overlaps an element in elements1.
func ElementOverlapPro... |
3e1319b806cad430aaf672f2014fadc4a3d48936fdb5ee1c4c7924bdffabfecd | Go | 8,698 | 315 | // Notes:
// set divBedDir = "/work/yl726/pfaDivBedOutputs", files like chr5.107183644.107184616.Consensus_HAQER_0316.bed
// set vcfDir = "/hpc/group/vertgenlab/raven/PrimateT2T_20way/selection_hs1/populationData/Filtered", files like chr22.segSite.vcf.gz
// (only for reference now, not used in program) divSegDir = ... |
4c4f052444054248b0461575806f213062a635be487cda4189ca583108b9a08f | Go | 8,743 | 209 | // Command Group: "Variant Calling & Annotation"
// A tool to find variation between multiple alignment files
package main
import (
"errors"
"flag"
"fmt"
"log"
"path/filepath"
"strings"
"sync"
"time"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/g... |
c1df30e2ac63da2e6b9ba3bfb0aa3810c8d670e1df2665f1b8df4b1289613cc0 | Go | 8,748 | 196 | package main
import (
"os"
"testing"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
)
func TestAllPossibleOneHumanNonGeneric(t *testing.T) {
var err error
var hum fasta.Fasta = fasta.Fasta{Name: "h... |
038d6b530e3b0e1d7e550ca834854be2f0b85864bde571796b04048833ef1000 | Go | 8,774 | 238 | package sam
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
)
var DiploidBaseCallFromPileTests = []struct {
P Pile
RefBase dna.Base
Delta float64
Gamma float64
Epsilon float64
Lambda float64
Expected DiploidBase
}{
{P: Pile{CountF: [13]int{16, 14, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0}},... |
f2158a3e3c6e3c72903fd24f3c78619412e58b79e75bb310184f0dd56183fa32 | Go | 8,849 | 342 | package sam
import (
"bytes"
"encoding/hex"
"io"
"log"
"math"
"strconv"
"strings"
"github.com/vertgenlab/gonomics/bgzf"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/exception"
)
// BamWriter wraps a bgzf.BlockWriter and provides functions to write
// a Sam struct to a binary Bam f... |
f8b5bc9785cced3da398cb3e712ba8997bbc986d00d4b2b43b2f4d61ca706fb0 | Go | 8,917 | 218 | package popgen
import (
"fmt"
"log"
"math"
"math/rand"
"os"
"runtime/pprof"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/logspace"
"golang.org/x/exp/slices"
)
// To access debug prints, s... |
d3f8f8c948ccb8a91deb356dec9a31dec987ec45b4740d86c3f860f5d44f79b1 | Go | 8,923 | 311 | // Command Group: "Sorting"
// Executes an external merge sort of the input file based on desired sort criteria
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/fastq"
"log"
"os"
"path"
"path/filepath"
"strings"
"github.com/vertgenlab/gonomics/axt"
"github.com/vertgenlab/gonomics/bed"
"g... |
96841fd64577871a8c9a5030437b5e1d666c02660d8032b8590ebc62608f44f2 | Go | 8,928 | 265 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
)
type Settings struct {
InFa string //input fasta file with 2 ali... |
341ab4cb5d777e67493d02dd89f776b9f30213c7a4b48bb7d86892eb4833d6c5 | Go | 9,028 | 234 | // Package lift provides an interface and utilities for working with genomic regions and offer flexibility to modify their coordinates.
package lift
import (
"github.com/vertgenlab/gonomics/axt"
"github.com/vertgenlab/gonomics/dna"
"io"
"log"
"path"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/g... |
6717c0085d7c445483fc6ab3ba9cc90b1fe4fef8b6c2ade68effa1cca5ce8b38 | Go | 9,055 | 202 | // Command Group: "FASTA and Multi-FASTA Tools"
// Using a four-way multiple alignment (including the reference species followed by three successive outgroups),
// this program calculates branch lengths in units of estimate substitutions for regions in the alignment specified by an input bed file
package main
import ... |
5eee25b3dfab82f7697a1b39c85feaecc7fd799e1a44b473c31118396a492ed3 | Go | 9,163 | 239 | package genomeGraph
import (
"fmt"
"math"
"strings"
"sync"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/giraf"
"github.com/vertgenlab/gonomics/numbers/parse"
"github.com/vertgenlab/gonomics/sam"
)
func ... |
853217486b0a9048df39f0baee53f3316139234a83b6910d5d54ad1dd7863954 | Go | 9,189 | 285 | package fit
import (
"github.com/vertgenlab/gonomics/numbers"
"log"
"math"
"math/rand"
)
// MixtureModel holds data, results, and working memory for running the EM algorithm.
type MixtureModel struct {
Data []float64 // 1d data slice
K int // number of component distributions
M... |
51da3e3e3e71bd406d9b0d3a1bb2eb1168e1bf43e221cb50b41bdfa77a3082e1 | Go | 9,202 | 242 | //Command Group: BED Tools
// geneAssignmentStats compares a bedpe containing a gene symbol in the name field to a test set of output from
// assignGenomeSpace command which assigns every base in the genome a closest gene either from proximity or from a 3d contact map.
package main
import (
"flag"
"fmt"
"github.co... |
c4782efcdafe869af03c6024af4368816fc4106e603f60a1357cd42956bd45f0 | Go | 9,209 | 275 | // Package chain declares the Chain struct that describes an alignment block and contains functions that operates on chain structs.
package chain
import (
"fmt"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fi... |
24a9ec533285c426918780b556dcd447b621085d8a9793cd1c1dd15ce044c732 | Go | 9,239 | 244 | // Command Group: "General Tools"
// Lifts a compatible file format between assembly coordinates
package main
import (
"flag"
"fmt"
"io"
"log"
"strings"
"unicode/utf8"
"github.com/vertgenlab/gonomics/chain"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenl... |
7518f2315ae4f0d7e8e03d1a395eee153475907a6d4ce34249bbc058f5845049 | Go | 9,529 | 255 | // Package ontology provides functions for gene ontology enrichment analysis.
package ontology
import (
"fmt"
"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/filei... |
c88e719493e14151315a8e8e8b87a9f7ced59bc04e0e85bbb58bd33ebf13b462 | Go | 9,585 | 299 | package binaryGiraf
import (
"bytes"
"encoding/binary"
"fmt"
"io"
"log"
"strings"
"github.com/vertgenlab/gonomics/bgzf"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/dna/dnaThreeBit"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertge... |
c722e13750cdfb9b4c95ddfc3480a8d5184eb8b554cc793472bb9a5f41f33f90 | Go | 9,590 | 271 | // Command Group: "Variant Calling & Annotation"
// Separates a sam alignment from a heterozygous individual
package main
import (
"flag"
"fmt"
"log"
"strings"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/vcf"
)
func usage() {
fmt.Print(
"alleleSplit - separates a sam alignment f... |
10f2ff364ef1d8d2ae873f0c46eda527fd748af8c0b0e086c05a49b967a82b19 | Go | 9,656 | 262 | // Command Group: "BED Tools"
// Options to alter bed formatting
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/convert"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"githu... |
349ba4a065f4ba8fcae9bcd484a9e197a00380d05dbb8577fc9a0f5d929a0ee4 | Go | 9,663 | 319 | package gene
import (
"errors"
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/numbers"
)
// Insertion adds bases to the Gene, predicts the effect, and updates the Gene struct to reflect the change.
// The position should be the base-zero genomic coordinate of the base directly BEFORE ... |
d2d92128bf38b014fe181adccc421e0d508c194ed8081aa2ea415666cddbce8c | Go | 9,784 | 352 | package main
import (
"fmt"
"os"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta/pFasta"
"github.com/vertgenlab/gonomics/fileio"
"testing"
)
var extractTests = []struct {
InFile string
Chrom string
OutName string
OutFile string
Start int
End ... |
23c5a7d440cc00ccc7cce73039b8271f7fab8ecc6945c5877e328ac49e9c2087 | Go | 9,810 | 266 | package dna
import (
"fmt"
"log"
"strings"
"testing"
)
var dnaStrings = []string{
"ACGTacgtNn",
"AAAAAACCCCCGGGGTTTTT",
"aaaaaCCCCTTTaaaaa",
"NNNNNAAAaaaTTT",
}
func TestDnaToFromString(t *testing.T) {
for _, input := range dnaStrings {
bases := StringToBases(input)
answer := BasesToString(bases)
if i... |
10ac70917d45ff515da7cc075e94d0df1c409f4c0a50f6a5fb653b898b871c07 | Go | 9,849 | 259 | package simulate
import (
"fmt"
"log"
"math/rand"
"strings"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/sam"
)
// IlluminaPairedSam generates pairs of sam reads ra... |
1e8a541e9fb95fd8d51665b8d14b90a4311e32586171cd5159da5eeb458ee082 | Go | 9,882 | 305 | package sam
import (
"bytes"
"encoding/binary"
"log"
"math"
"sort"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
// bai files are an index format for bam files
// Specs for bai can be found in section 5.2 on page 19 of:
// https://raw.githubusercontent.com/samtools/hts-s... |
86d170e83321df4034851914008e9fdf811a77d28f15c10309411e73815aafcb | Go | 9,931 | 272 | package browser
import (
"fmt"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta/pFasta"
"github.com/vertgenlab/gonomics/fileio"
"log"
"strings"
"unicode/utf8"
)
// PFaVisualizer produces command line visualizations of pFasta format alignments from a specified start and end posit... |
28e7aa065ab1100fd8cd069ada3a236de1e6d7efad93f2b7e572fcf3818a73d2 | Go | 10,044 | 290 | // Command Group: "BED Tools"
// Filters bedpe entries based on overlaps from the select file.
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/bed/bedpe"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.co... |
138212287a393f435154fc3fd26dc36480946fda9c323165bab762492a7f4ded | Go | 10,121 | 219 | package numbers
import (
"log"
"math"
"github.com/vertgenlab/gonomics/numbers/logspace"
)
// LogIntegrate evaluates log(int_a^b f(x)dx) in cases where f returns log(f(x)). Uses the rectangle rule.
func LogIntegrate(f func(float64) float64, a float64, b float64, n int) float64 {
if a >= b {
log.Fatalf("logInteg... |
7ad33dfbf4ff9d03589d5eb3d688a345119dc977473e62fab8db23d8353497f9 | Go | 10,124 | 357 | package browser
import (
"testing"
"github.com/vertgenlab/gonomics/dna/pDna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta/pFasta"
"github.com/vertgenlab/gonomics/fileio"
)
var PrintOneSetLinesTests = []struct {
LineLength int
SetOfLinesIdx int
NumIters int
LineA ... |
1c847256351869ce1851e2148b2ad73ed9628afeffffb72100f8d0c5a82e1744 | Go | 10,225 | 356 | // Package maf provides structs and functions for processing alignments in maf format.
// The file format is described more here: https://genome.ucsc.edu/FAQ/FAQformat.html
package maf
import (
"fmt"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fil... |
181e587b641e0982f0e3d7ba61d4e84f99ed174bec1b5730c1148ca1fd4c7702 | Go | 10,269 | 264 | package simulate
import (
"fmt"
"log"
"math"
"math/rand"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
)
// RandIntergenicSeq makes a randomly generated D... |
d346a0bd7be077623daa1802071e3cf7b095df585d7408d6176149ed5033d921 | Go | 10,302 | 287 | // Package obo provides functions for reading, writing, and manipulating Open Biomedical Ontologies (obo) format files.
// This package follows the OBO Flat File Format 1.4, as specified here: http://owlcollab.github.io/oboformat/doc/obo-syntax.html
package obo
import (
"fmt"
"io"
"log"
"strings"
"github.com/ver... |
9ec6968e5a0f6bc1224a6036c1e516146b3b5f80a1f2ca352d54c14ac56f27d5 | Go | 10,343 | 311 | // Package expandedTree contains structs and functions that build and utilize information in a binary tree format that can be used for genome simulation and reconstruction
package expandedTree
import (
"errors"
"fmt"
"log"
"strconv"
"strings"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics... |
f76f0ee333c9a110d4cb3e943bcd547a785a864e211315bab8e8f40e4163185a | Go | 10,379 | 189 | // Command Group: "Data Conversion"
// Uses globalAlignment, affineGap (instead of constGap) to align 2 .fasta files, each with only 1 sequence, then convert cigars to ins and del beds
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/align"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertg... |
4175d3a8024f4bfb023424dc5671ce7b186be74e571e44976d7d77c92d057e16 | Go | 10,442 | 336 | package sam
import (
"bytes"
"errors"
"io"
"log"
"strings"
"github.com/vertgenlab/gonomics/bgzf"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
)
// bam is a binary version of sam compressed as a bgzf file
// specs can be found in the s... |
e6198e5272636faf91eca8e3a170d36a58d712066f018ee0e1320339eacdce18 | Go | 10,503 | 266 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/numbers"
"log"
"os"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/sam"
)
// PriorSettings defin... |
c045be32101361aff0d93e7eef41f67094ce8728382e9586832ae7eb41d32a2d | Go | 10,794 | 375 | // Command Group: "VCF Tools"
// Provides summary statistics on an input VCF file
package main
import (
"flag"
"fmt"
"io"
"log"
"strings"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.co... |
2cba2e3d8bac193e50fc50bf6cc3df0ab8c3cf2dd87b5d40793837514bb8adf6 | Go | 10,865 | 284 | package variant
import (
"github.com/vertgenlab/gonomics/dna"
)
// CodingChange describes a change of a protein sequence caused by
// a mutation affecting the coding sequence of the corresponding gene.
// CodingPos and ProteinPos refer to the zero-based start position of
// the change. The CodingPos always refers to... |
0684b077742648357d3899a6c5647282e53147523140880538c8177557aa7b51 | Go | 10,961 | 402 | package sam
import (
"bytes"
"encoding/hex"
"errors"
"fmt"
"github.com/vertgenlab/gonomics/exception"
"log"
"math"
"strconv"
"strings"
)
// QueryTag returns the value of tag t for read s. Currently QueryTag
// is only supported if the sam was read from a bam file. If no tag
// data is present, or if the reco... |
79bd10fc6cb834081682fc2f72f0745add8779ea8e2daeb24c9e2aae2fe7cd2e | Go | 10,980 | 431 | package dna
import (
"errors"
"log"
"strings"
)
// Codon is an array of three DNA bases for genetic analysis of proteins and amino acids.
type Codon [3]Base
// AminoAcid converts the twenty canonical amino acids and stop codon into bytes.
type AminoAcid byte
const (
Ala AminoAcid = 0
Arg AminoAcid = 1
Asn ... |
7fdfa098c95f13c6fe378fc3bba6acfa90c9dac933e98598a87b26aa050458e2 | Go | 11,068 | 254 | package popgen
import (
"log"
"math"
"strings"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/logspace"
"github.com/vertgenlab/gonomics/vcf"
)
/*
This file implements functions to construct a Hierarc... |
7cfc5132ad43f652e4c124b831d396e7157c8e560663a2a9c053223515e48452 | Go | 11,250 | 392 | package interval
import (
"io"
"math/rand"
"testing"
"time"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/numbers"
)
func TestQuery(t *testing.T) {
type testQuery struct {
query *bed.Bed
relationship string
hasOverlap bool
}
var targetIntervals []Interval = []Interval{... |
1fc4808c430a9f72177a7a6542f1619c76f8c28c708d5b6b34d8246377e99e14 | Go | 11,375 | 244 | // Command Group: "Statistics & Population Genetics"
// Performs velocity and acceleration on a four way multiple alignment in multiFa format
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.co... |
37e5c6f5d43597704ec9237449e806b42270712bdb106f45863beb53219b987d | Go | 11,387 | 339 | package main
import (
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"math"
"os"
"testing"
)
var WigMathTests = []struct {
InFile string
OutFile string
ChromSizes string
BedMask string
MinValue float6... |
0b0a23153d66b3193cf5f71e3fa70cd0b8187c2656204971ce96b4c85796e0a0 | Go | 11,438 | 246 | // Command Group: "Statistics & Population Genetics"
// Returns the p-value of enrichment and depletion for overlaps between the elements in two input files
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/numbers"
"log"
"github.com/vertgenlab/gonomics/exc... |
1bcc29b2521ddb9c6d0f4d9c7826f2f466d882c6a558f66b1fa46fca7854e3c0 | Go | 11,463 | 318 | // Notes:
// CLI inputs below
// bedFile == /hpc/group/vertgenlab/raven/PrimateT2T_20way/aqers/T2T/niceName/human.bed, Consensus HAQER bed, 1596 lines, column 4 is HAQER name/ID
// pfaDir == /hpc/group/vertgenlab/raven/PrimateT2T_20way/work/yl726/PrimateT2T_20way/haqerTmp.humanT2T, files like chr22.pFa.gz
// outDir == ... |
f4587b783ecb9df9013a43a5a0efa01ffec4fab6af22b7fa7551111f3b1a5ae0 | Go | 11,514 | 246 | // Command Group: "Statistics & Population Genetics"
// Returns a tab separated list of function evaluations for plotting functions
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/parse"
"github.com/vertgenlab/gonomics/popgen"
"log"
"strings"
... |
a0b8bb45d29c2b8fdbe99fd0f9c433c1be6ef5631041af19fa5386edd35f775a | Go | 11,551 | 378 | package gene
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/gtf"
)
func TestDeletion(t *testing.T) {
g := gtf.Read("testdata/test.gtf")
f := fasta.Read("testdata/test.fasta")
var err error
gene := GtfToGene(g["test_gene_id"], f)... |
cae6386f1e0cdbfcfd5525911a805cab9b90dcd46e507a09ccba769eed0c6eca | Go | 11,688 | 202 | package sam
import (
"log"
"math"
"github.com/vertgenlab/gonomics/numbers/logspace"
)
// AncientLikelihoodCache stores the following short expressions from the likelihood functions to
// save on repeated logspace.Pow calls.
type AncientLikelihoodCache struct {
EpsilonOverThree []f... |
1617cd570c176ed0bd16a4f4c79cc70af5ce7d64bb270be2eaa68512c649133d | Go | 11,756 | 258 | // Command Group: "General Tools"
// Write out lastZ pairwise inputs using contig alignment where multiple references are being used
package main
import (
"flag"
"fmt"
"log"
"os"
"path"
"path/filepath"
"strings"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/lastZWriter"
)
// MakeA... |
c974b418049e3205824e641fd3f84904b89abbc80daaf4e626446b2c0770ec4b | Go | 11,858 | 334 | // Package gtf contains functions for reading, writing, and manipulating GTF format files.
// More information on the GTF file format can be found at http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format
// Structs in the GTF package are organized hierarchically, with the gene struct containing the underlying... |
9a980a7974983404943d667048fdbca673b2191612e60b91dae9c0d24bd2ea5d | Go | 11,875 | 303 | package motif
import (
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/dna/dnaTwoBit"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"log"
"math"
)
// ScoreWindow returns... |
d69957a37021824244d903312a3e216fa29394c2fdddc4e7a26e90e3a7d1f6ef | Go | 11,898 | 336 | package genomeGraph
import (
"log"
"sync"
"testing"
"time"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/giraf"
)
func TestWorkerWithWriting(t *testing.T) {
var output string = "testdata/pairedTest.giraf"
var tileSize int = 32
var stepSize in... |
e9979b1fb1ac23a8dc1898987e84f4ec6cd76c2312a14568b7dda8f98396bdf3 | Go | 11,920 | 343 | package genomeGraph
import (
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/parse"
"github.com/vertgenlab/gonomics/vcf"
"log"
"strings"
)
func VariantGraph(ref <-chan fasta.Fasta, vcfMap map[string][]v... |
9bc0553e0fbd14995c3cf9612f224f96910402d4e175ee05fdf5f7551a01fbcb | Go | 11,966 | 384 | package vcf
import (
"fmt"
"io"
"log"
"strconv"
"strings"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
// Header contains all information present in the header section of a VCF.
// Info, Filter, Format, and Contig lines are pa... |
f20f0972d354f19d12947be0f9aa684535c34f492de8faa42fe52e7f069c388d | Go | 12,113 | 324 | // Command Group: "Statistics & Population Genetics"
// Command line statistics calculator
package main
import (
"flag"
"fmt"
"log"
"math/rand"
"strings"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomic... |
aa39796a02bdd2733afce3ebebf11e4eae60d9ed538ce7ee2abf16860950a1c7 | Go | 12,430 | 338 | // Command Group: "Data Conversion"
// Generates a fasta file from a sam over a reference sequence
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/sam"
)
type Settings struct {
SamFileName string
RefF... |
c28e3f330bc098c64470dc35adc740cdadfbe205a9c81b0e62512d92816f7346 | Go | 12,487 | 382 | package gene
import (
"testing"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/gtf"
)
func TestInsertion(t *testing.T) {
g := gtf.Read("testdata/test.gtf")
f := fasta.Read("testdata/test.fasta")
var err error
gene := GtfToGene(g["test_gene_id"], f... |
692d3973c292b500f12b28d60f31ba5c981f5af27f9890f77a6edb534d392c22 | Go | 12,544 | 382 | package vcf
import (
"log"
"strconv"
"strings"
"github.com/vertgenlab/gonomics/exception"
)
// ParseInfo parses the data stored in vcf.Info.
// Fills an unexported map in the Vcf struct
// that can be queried with Query(type) functions.
func ParseInfo(v Vcf, header Header) Vcf {
v.parsedInfo = make(map[string]i... |
7ac91026c07a6f28d4f3713623ffd3b1cb03d817a5b0ef8c069723a72a38c6af | Go | 12,756 | 311 | package ontology
import (
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/bed/bedpe"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/interval"
"github.com/vertgenlab/gonomics/numbers"
"log"
)
// Fill3dSpace takes in a set of Bedpe format contact points, single-bas... |
ec1264b69949affe0cc6b7e8f2056995f19d828e3b3225c616671c57265e3c97 | Go | 12,874 | 312 | // Command Group: "Data Conversion"
// Convert HiC contact maps in straw format to bedpe contact peak calls
package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/bed/bedpe"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"gith... |
c9c3d1fc54e7a27c84fe6b6d7799a0038170bd7a0203f86a4fa466e165a01ae8 | Go | 13,022 | 316 | package sam
import (
"fmt"
"log"
"math"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/logspace"
)
// InsertionType encodes the insertion genotype state, which can be one of the four constant values explained below.
type InsertionType byte
... |
45c835a737a193d76b6a16cf6316da7efa5e9f9f339b74fbd1f9b842e0551394 | Go | 13,413 | 410 | package main
import (
"fmt"
"log"
"math/rand"
"strconv"
"strings"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/popgen"
"github.com/vertgenlab/gonomics/simulate"
)
// SimMain function to be called in si... |
277ad609bb4bda9d632dccace327da5ab0b4afba4e574c4e71a0aa0ee5b9f9d7 | Go | 13,716 | 374 | package numbers
import (
"fmt"
"log"
"math"
"github.com/vertgenlab/gonomics/numbers/logspace"
"github.com/vertgenlab/gonomics/numbers/parse"
)
// NormalDist returns the normal distribution value x for a distribution with mean mu and standard deviation sigma.
func NormalDist(x float64, mu float64, sigma float64)... |
a3a9f7cf32b97056b288827d34241b67fe920622c187553a87567d2403926111 | Go | 13,919 | 448 | // Package interval provides functions for manipulating and analyzing intervals including
// sorting, calculating overlaps, and liftover functions.
package interval
// Adapted from Mao, Eran & Luo 2019
// DOI: 10.1038/s41598-019-41451-3
import (
"fmt"
"sort"
"golang.org/x/exp/slices"
)
// Interval is a type inte... |
b20ad2a315ea63ab28b43965e7c2564cdcbc4b0a5c1120262400244c9f79ead8 | Go | 13,991 | 342 | 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"
"github.com/vertgenlab/gonomics/wig"
"log"
"math"
"math/rand"
"os"
"sort"
)
// MathSettings defines the usage ... |
2a11efaefcf15e9a04f8230d3c2fff6d23f8b6e8192e8c571814be52abcd929f | Go | 14,052 | 351 | package genomeGraph
import (
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/dna/dnaTwoBit"
"github.com/vertgenlab/gonomics/fastq"
"github.com/vertgenlab/gonomics/numbers"
)
func extendToTheRight(node *Node, read fastq.FastqBig, readStart int, nodeStart int, posStrand bool) []*SeedDev... |
da02bff1565738f3c05b30027bd572b221ee173d8645c02f2fee135fc82a83f3 | Go | 14,165 | 477 | package main
import (
"flag"
"fmt"
"log"
"os"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/sam"
)
type ScoreSettings struct {
ScoreType string
InFileList strin... |
c955d2a93b5789a86a43592d1a74dcde24237977cdde282a482c6118a2891b5c | Go | 14,641 | 320 | package motif
import (
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
"log"
"math"
)
type MatchCompSettings struc... |
17aea9a47a3dc195fe74141265596e78a42152abe9285ab40f073d054f1e2216 | Go | 14,664 | 361 | package main
import (
"flag"
"fmt"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/convert"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"log"
"strings"
)
type Settings stru... |
3b0e1b4beac77ef1a34d490b54e593a1c665aa2d8648967029ef924f56e629bc | Go | 14,677 | 458 | package sam
import (
"fmt"
"io"
"log"
"strconv"
"strings"
"sync"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
)
// readSamToChan streams the input Sa... |
dd46b31a930d565036474f1ad17973e437267929ae2498ea4c5413578016c7b0 | Go | 15,182 | 476 | package sam
import (
"fmt"
"log"
"github.com/vertgenlab/gonomics/chromInfo"
"github.com/vertgenlab/gonomics/cigar"
"github.com/vertgenlab/gonomics/dna"
)
// Pile stores the number of each base observed across multiple reads.
// The number of a particular base can be retrieved by using the dna.Base
// as the ind... |
9bac007cd3f626d44ee862d4df8d71f4497620329354e87e7614b18025e452bf | Go | 15,483 | 364 | package sam
import (
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/logspace"
"github.com/vertgenlab/gonomics/numbers/parse"
"log"
"math"
"strings"
)
type DiploidBase byte
const (
AA DiploidBase = ... |
3e64a73dfcfd260797b281e9a7a00b7c467f62a30102da22df10043b63cdd842 | Go | 15,656 | 482 | // Command Group: "VCF Tools"
// Filter vcf records
package main
import (
"flag"
"fmt"
"log"
"math"
"math/rand"
"strings"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/popgen"
"github.com/vertgenlab/gonomics/vcf"
)
// coordinate is a chr... |
c4ccdc8e6e4d25883c94191b4ffcb94093b45b16069b79f21a3e04d4df11646a | Go | 15,816 | 521 | // 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... |
68f199927622f18a99b16c4446eaa644f5aa1b3010f57742d9e3c5675370b799 | Go | 16,006 | 453 | package fasta
import (
"github.com/vertgenlab/gonomics/dna"
"log"
// "fmt"
)
// RefPosToAlnPos returns the alignment position associated with a given reference position for an input MultiFa. 0 based.
func RefPosToAlnPos(record Fasta, RefPos int) int {
var refStart, alnStart = 0, 0
for t := alnStart; refStart < R... |
2045e7e2d1a1c252b308c34a4c20531e17abc61883a640af2a2e9866496f6077 | Go | 16,120 | 457 | package gene
import (
"errors"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/numbers"
)
var (
ErrNoStopFound = errors.New("frameshift was unable to find a stop before the end of the gene")
)
// Deletion removes bases from the Gene, predicts the effect, and updates the Gene struct to refle... |
3d631d33f64e50e764799d9fa1b41546adf6a70761c4b18e4f541b8d720275df | Go | 16,326 | 343 | package fit
import (
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/logspace"
"log"
"math"
"math/rand"
)
// direction is a type used to define the heading in coordinate ascent.
type direction byte
const (
neutral direction = 0
north direction = 1
northeast direction = ... |
eab62dded1b9138158b67aeb9f30fd1db9cd8499349b212fb69cb685de2fad95 | Go | 16,425 | 385 | package align
import (
"fmt"
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
)
// the trace data structure is a 3d slice where the first index is 0,1,2 and represents the match, gap in x (first seq), and gap in y (second seq).
// m used to have the same data structure as trace, ... |
77295e3f97fc16342c2ded6a36da280d9734b4ff88c732fff70955a00307354d | Go | 16,530 | 400 | // Package reconstruct has tools for reconstructing ancient genomes from the genomes of extant species using newick trees and fasta files.
package reconstruct
import (
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/dna/pDna"
"github.com/vertgenlab/gonomics/expandedTree"
"github.com/ve... |
0439f37701b7acef5fc74596cdd22dfac5f34c9ea9c435175543b1ef51200a8f | Go | 16,650 | 369 | // Package convert contains functions for converting data between standard file formats. This is a high level package that avoids circular dependencies.
package convert
import (
"log"
"github.com/vertgenlab/gonomics/bed"
"github.com/vertgenlab/gonomics/bed/bedGraph"
"github.com/vertgenlab/gonomics/chromInfo"
"gi... |
99f575c13a5b5f29f00f486e2a031e35a5e5a589774ba2c01cdecb8655fb511e | Go | 16,791 | 346 | // Package phylo contains functions related to phylogenetic analysis from multiple sequence alignment data.
package phylo
import (
"log"
"math"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/numbers"
)
// AccelDistancesAndWeights represents a set of a... |
d0db2ab53ece3c6a8d0a1a2bc531c7c2a5b791da51674ae9c3c1f74bdec57c65 | Go | 16,915 | 520 | package main
import (
"fmt"
"sort"
"strconv"
"strings"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/sam"
"github.com/vertgenlab/gonomics/vcf"
)
type variantType... |
1460dd06a5c10524bd1910d87359a507fcb8eab31f36bc88965fab6507d1ae65 | Go | 17,138 | 507 | package gtf
import (
"fmt"
"math"
"strings"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/numbers"
)
// VariantToAnnotation generates an annotation which can be appended to the INFO field of a VCF
// Annotation format is: GoEP= Genomic | Gene | cDNA | Protein | VariantType
// Genomic cDNA... |
2e994739291fcdd55d61e892387e2422a381a19f0f616aa4ff9dda0e9b100c35 | Go | 17,381 | 427 | // Command Group: "Sequence Evolution & Reconstruction"
// WARNING: this program is now deprecated. Please use 'reconstructSeq' as its replacement.
// Returns maximum likelihood sequence from an HBCGO primate alignment
package main
import (
"flag"
"fmt"
"log"
"github.com/vertgenlab/gonomics/dna"
"github.com/ver... |
8c08771adf22912106ab47072a8b940f22861ffeadfe22591a438e590b31388d | Go | 18,209 | 546 | package gtf
import (
"fmt"
"math"
"reflect"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/interval"
"github.com/vertgenlab/gonomics/vcf"
)
type vcfEffectPrediction struct {
vcf.Vcf
RefId string // e.g. NC_000023.10, LRG_199, NG_012232.1, NM_004006.2, LRG-199t1, NR_002196.1, NP... |
659b204f190e22081363ac116fd323d5f152a2c67d48a268dc6fc2d5d41a7e5e | Go | 19,036 | 289 | package main
import (
"fmt"
"github.com/vertgenlab/gonomics/dna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/logspace"
"log"
"math"
)
// incrementWind... |
a33d8378b404331c722357ccddc219ca4e4eee2fcd81e2b2dd31bcd723139083 | Go | 19,436 | 456 | package variant
import "github.com/vertgenlab/gonomics/dna"
// Reference sequence used in the following tests
//
// Seq Idx : 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
// CDS Idx : 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
// Seq : C A A T G C A... |
f42f746213091ff67450dc1f0ad3fa078254d61aa3ff0bdfd387990004f7de53 | Go | 19,702 | 322 | package main
import (
"fmt"
"log"
"math"
"strings"
"github.com/vertgenlab/gonomics/dna/pDna"
"github.com/vertgenlab/gonomics/exception"
"github.com/vertgenlab/gonomics/fasta/pFasta"
"github.com/vertgenlab/gonomics/fileio"
"github.com/vertgenlab/gonomics/numbers"
"github.com/vertgenlab/gonomics/numbers/logsp... |
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