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vcfRead.go
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vcfRead.go
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package vcfio
import (
"bufio"
"bytes"
"errors"
"fmt"
"log"
"os"
"strconv"
"strings"
"github.com/biogo/hts/bgzf"
)
// ReadVcf reads VCF file into stream for irelate
func ReadVcf(vcfFile string) (*VcfReader, error) {
// Open VCF file
rdr, err := os.ReadFile(vcfFile)
if err != nil {
return nil, err
}
byteRdr := bytes.NewReader(rdr)
// Presumes VCF with denormalized variants ("bcftools norm -m -any"), bgzipped and tabix indexed
qrdr, err := bgzf.NewReader(byteRdr, 0)
if err != nil {
newErr := fmt.Errorf("error opening query file %s: %s", vcfFile, err)
return nil, newErr
}
// Parse VCF file with vcfgo to use in irelate
vcfRdr, err := NewVcfReader(qrdr)
if err != nil {
log.Fatalf("error parsing VCF query file %s: %v", vcfFile, err)
}
return vcfRdr, nil
}
// ReadNewVcf returns a Scanner to iterate over VCF records and the parsed Header.
// It assumes denormalized variants (bcftools norm -m -any)
func ReadNewVcf(vcfFile string) (*bufio.Scanner, *Header, error) {
// Open VCF file
rdr, err := os.ReadFile(vcfFile)
if err != nil {
return nil, nil, err
}
byteRdr := bytes.NewReader(rdr)
bgzipReader, err := bgzf.NewReader(byteRdr, 0)
if err != nil {
newErr := fmt.Errorf("error opening query file %s: %s", vcfFile, err)
return nil, nil, newErr
}
s := bufio.NewScanner(bgzipReader)
header, err := parseHeader(s)
if err != nil {
return nil, nil, err
}
return s, header, nil
}
// parseHeader will read the scanner lines until it reaches
// the '#CHROM' line. Every conditional aims to parse specific
// information from the VCF header.
func parseHeader(s *bufio.Scanner) (*Header, error) {
header := NewHeader()
for s.Scan() {
line := s.Text()
if strings.HasPrefix(line, "##fileformat") {
v, err := parseHeaderFileVersion(line)
if err != nil {
log.Println(err)
}
header.FileFormat = v
} else if strings.HasPrefix(line, "##FORMAT") {
format, err := parseHeaderFormat(line)
if err != nil {
log.Println(err)
}
if format != nil {
header.SampleFormats[format.Id] = format
}
} else if strings.HasPrefix(line, "##INFO") {
info, err := parseHeaderInfo(line)
if err != nil {
log.Println(err)
}
if info != nil {
header.Infos[info.Id] = info
}
} else if strings.HasPrefix(line, "##PLATFORM") {
kv := strings.Split(line, "=")
if len(kv) == 2 {
header.Platform = kv[1]
}
} else if strings.HasPrefix(line, "##FILTER") {
filter, err := parseHeaderFilter(line)
if err != nil {
log.Println(err)
}
if len(filter) == 2 {
header.Filters[filter[0]] = filter[1]
}
} else if strings.HasPrefix(line, "##contig") {
contig, err := parseHeaderContig(line)
if err != nil {
log.Println(err)
}
if contig != nil {
if _, ok := contig["ID"]; ok {
header.Contigs = append(header.Contigs, contig)
} else {
log.Println("bad contig", contig)
}
}
} else if strings.HasPrefix(line, "##SAMPLE") {
sample, err := parseHeaderSample(line)
if err != nil {
log.Println(err)
}
if sample != "" {
header.Samples[sample] = line
} else {
if err != nil {
log.Println(err)
}
}
} else if strings.HasPrefix(line, "##PEDIGREE") {
header.Pedigrees = append(header.Pedigrees, line)
} else if strings.HasPrefix(line, "##") {
kv, err := parseHeaderExtraKV(line)
if err != nil {
log.Println(err)
}
if len(kv) == 2 {
header.Extras = append(header.Extras, line)
}
} else if strings.HasPrefix(line, "#CHROM") {
var err error
header.SampleNames, err = parseSampleLine(line)
if err != nil {
log.Println(err)
}
break
} else {
e := fmt.Errorf("unexpected header line: %s", line)
return nil, e
}
}
return header, nil
}
// ExtractVcfFields parses basic information about variant
func ExtractVcfFields(chr string, start int, ref, alt string, info *InfoByte) (VariantInfo, error) {
var vcf VariantInfo
// Empty Alt
if alt == "." || alt == "" {
log.Println("Alt is empty", vcf, info)
return vcf, nil
}
// SVtype
var svtype string
svtypeInterface, err := info.Get("SVTYPE")
if err != nil && !strings.Contains(err.Error(), "not found in header") {
log.Printf("Error getting SVType from INFO\n%v\n%v\n", info, err)
}
if err == nil {
svtype = svtypeInterface.(string)
}
// Alt, End
switch {
// Deletion or Duplication
// Duplication "1 14621 . N <DUP> 5.56 LOWBFSCORE SVTYPE=DUP;END=17098;EXPECTED=175;OBSERVED=250;RATIO=1.43;BF=5.56 GT 0/1"
// Inversion - ex. "2 321682 INV0 T <INV> 6 PASS SVTYPE=INV;END=421681"
// LOH - "chr22 44084517 . N <LOH> . PASS CN=2;CS=10;SVTYPE=LOH;END=50776368;NUMSNP=2405 GT ./."
case svtype == "DEL" || svtype == "DUP" || svtype == "INV" || svtype == "LOH":
var end int
endInterface, err := info.Get("END")
if err != nil && !strings.Contains(err.Error(), "not found in header") {
log.Println("Error getting END from INFO", info, err)
} else if endInterface != nil {
end = endInterface.(int)
} else {
svLength, err := info.Get("SVLEN")
if err != nil {
log.Println("Error getting SVLEN from INFO", info, err)
}
if svLength != nil {
end = start + svLength.(int)
} else {
return vcf, errors.New("structural variant without identifiable END")
}
}
vcf = VariantInfo{
VariantKey: fmt.Sprintf("%s-%d-%d-%s", strings.Replace(chr, "chr", "", 1), start+1, end, svtype),
Chr: chr,
Start: start,
End: end,
Ref: "",
Alt: "",
IsSV: true,
SVtype: svtype,
}
// ex. 2 321681 . G G]2 : 421681] 0 PASS SVTYPE=BND;MATEID=bnd_U;EVENT=INV0
case svtype == "BND":
translocatedChr, translocatedStart, translocatedIsPosStrand, translocatedComesAfter := parseBreakendAlt(alt)
vcf = VariantInfo{
VariantKey: fmt.Sprintf("%s-%d-%d-%s", strings.Replace(chr, "chr", "", 1), start+1, start+len(ref), svtype),
Chr: chr,
Start: start,
End: start + 1, // Simple (wrong) assumption with little consequence right now
Ref: "",
Alt: "",
IsSV: true,
SVtype: svtype,
TranslocatedChr: translocatedChr,
TranslocatedStart: translocatedStart,
TranslocatedIsPosStrand: translocatedIsPosStrand,
TranslocatedComesAfter: translocatedComesAfter,
}
// ex. 13 321682 INS0 T C<ctg1 > 6 PASS SVTYPE=INS
case svtype == "INS":
vcf = VariantInfo{
VariantKey: fmt.Sprintf("%s-%d-%d-%s", strings.Replace(chr, "chr", "", 1), start+1, start+1, svtype),
Chr: chr,
Start: start,
End: start + 1,
Ref: ref,
Alt: "",
IsSV: true,
SVtype: svtype,
}
// NOTHING YET FOR:
// "INS:ME": InsertionMobileElement,
// "CNV": CopyNumberVariation,
case svtype != "":
vcf = VariantInfo{
VariantKey: fmt.Sprintf("%s-%d-%d-%s", strings.Replace(chr, "chr", "", 1), start+1, start+len(ref), svtype),
Chr: chr,
Start: start,
End: start + len(ref),
Ref: ref,
Alt: "",
IsSV: true,
SVtype: svtype,
}
default:
alt = strings.ToUpper(strings.Replace(alt, ".", "", -1))
vcf = VariantInfo{
VariantKey: fmt.Sprintf("%s-%d-%s-%s", strings.Replace(chr, "chr", "", 1), start+1, ref, alt),
Chr: chr,
Start: start,
End: start + len(ref),
Ref: ref,
Alt: alt,
IsSV: false,
SVtype: svtype,
}
}
return vcf, nil
}
// The assertion is that ref is replaced with t, and then some piece starting at position p is joined to t. The cases are:
// ALT Example Meaning
// t[p[ G[2 : 421681[ piece extending to the right of p is joined after t
// t]p] A]2 : 321681] reverse comp piece extending left of p is joined after t
// [p[t [2 : 321682[C reverse comp piece extending right of p is joined before t
// ]p]t ]2 : 321681]A piece extending to the left of p is joined before t
func parseBreakendAlt(altStr string) (joinedChr string, joinedStart int, joinedIsPosStrand, joinedIsAfter bool) {
var sep string
if strings.Contains(altStr, "[") {
sep = "["
} else {
sep = "]"
}
pt := strings.Split(altStr, sep)
t := strings.Split(pt[1], ":")
joinedChr = strings.TrimSpace(t[0])
posStr := strings.TrimSpace(t[1])
joinedStart, _ = strconv.Atoi(posStr)
joinedStart--
switch {
case strings.HasSuffix(altStr, "["):
joinedIsPosStrand = true
joinedIsAfter = true
case strings.HasSuffix(altStr, "]"):
joinedIsAfter = true
case strings.HasPrefix(altStr, "["):
joinedIsPosStrand = true
// case strings.HasPrefix(altStr, "]"):
}
return
}