func load_seq(h autoio.AutoioHandle) {
//fold := 50
for h.ReadScan() {
l := h.ReadText()
if len(l) == 0 {
continue
}
g_seq = l
}
g_seq = strings.ToLower(g_seq)
}
func load_tagset(h autoio.AutoioHandle) error {
line_no := 0
for h.ReadScan() {
line_no++
l := h.ReadText()
if len(l) == 0 {
continue
}
fields := strings.Split(l, ",")
if len(fields) != 2 {
return fmt.Errorf("bad read on line %s", line_no)
}
g_tagset[fields[0]] = fields[1]
g_tagseq[fields[1]] = fields[0]
}
return nil
}
func convert(gff_ain *autoio.AutoioHandle, ref_ain *simplestream.SimpleStream, aout *os.File, start_pos int64, allele_num int) error {
var e error
bufout := bufio.NewWriter(aout)
defer bufout.Flush()
for gff_ain.ReadScan() {
l := gff_ain.ReadText()
if len(l) == 0 || l[0] == '#' {
continue
}
gff_parts := strings.Split(l, "\t")
if len(gff_parts) < 9 {
return fmt.Errorf("not enough gff parts")
}
chrom := gff_parts[0]
_ = chrom
typ := gff_parts[2]
spos1ref, e0 := strconv.ParseInt(gff_parts[3], 10, 64)
epos1ref, e1 := strconv.ParseInt(gff_parts[4], 10, 64)
info := gff_parts[8]
// REFERENCE CHECK
//
gff_ref_seq := make([]byte, 0, 8)
idx := strings.Index(info, ";ref_allele ")
if idx >= 0 {
idx += len(";ref_allele ")
for ; idx < len(info); idx++ {
if info[idx] == 'a' || info[idx] == 'A' ||
info[idx] == 'c' || info[idx] == 'C' ||
info[idx] == 'g' || info[idx] == 'G' ||
info[idx] == 't' || info[idx] == 'T' ||
info[idx] == '-' {
gff_ref_seq = append(gff_ref_seq, info[idx])
} else {
break
}
if gff_ref_seq[len(gff_ref_seq)-1] == '-' {
break
}
}
}
g_GFF_REF = gff_ref_seq
//
// REFERENCE CHECK
alt_seq := ""
del_n := epos1ref - spos1ref + 1
spos0ref := spos1ref - 1
if typ != "REF" {
info_parts := strings.Split(info, ";")
alleles_info := info_parts[0]
if len(alleles_info) < 2 {
return fmt.Errorf(fmt.Sprintf("Invalid alleles info (%s)", info))
}
alts := strings.Split(alleles_info, " ")
alt_seqs := strings.Split(alts[1], "/")
if len(alt_seqs) == 0 {
alt_seq = alt_seqs[0]
} else {
if allele_num < len(alt_seqs) {
alt_seq = alt_seqs[allele_num]
} else {
alt_seq = alt_seqs[0]
}
if alt_seq == "-" {
alt_seq = ""
}
}
}
if e0 != nil {
return e0
}
if e1 != nil {
return e1
}
if start_pos < 0 {
if gVerboseFlag {
fmt.Printf("\n{\"comment\":\"initializing start_pos=%d\"}\n", spos0ref)
}
start_pos = spos0ref
}
if start_pos < spos0ref {
e = emit_nocall(start_pos, spos0ref-start_pos, ref_ain, bufout)
if e != nil {
return e
}
start_pos = spos0ref
}
if typ == "REF" {
e = emit_ref(start_pos, del_n, ref_ain, bufout)
if e != nil {
return e
}
start_pos += del_n
} else {
//DEBUG
//if int(del_n) != len(alt_seq) { fmt.Printf("\n>>>>> [%d] del_n %d, alt_seq %s (%d)\n", start_pos, del_n, alt_seq, len(alt_seq)) }
e = emit_alt(start_pos, del_n, alt_seq, ref_ain, bufout)
if e != nil {
return e
}
start_pos += del_n
}
}
return nil
}
func LoadSampleFastj(scan *autoio.AutoioHandle) ([][]TileInfo, error) {
line_no := 0
cur_seq := make([]byte, 0, 1024)
tilepath := -1
tilestep := -1
tilevar := -1
nocall := 0
_ = nocall
allele_path := make([][]TileInfo, 2)
for i := 0; i < len(allele_path); i++ {
allele_path[i] = make([]TileInfo, 0, 1024)
}
var first_tile bool = true
var tileid string
var s_tag string
var e_tag string
var md5sum_str string
var span_len int
var start_tile_flag bool
var end_tile_flag bool
for scan.ReadScan() {
l := scan.ReadText()
line_no++
if len(l) == 0 {
continue
}
if l[0] == '\n' {
continue
}
if l[0] == '>' {
// store tile sequence
//
if !first_tile {
m5 := Md5sum2str(md5.Sum(cur_seq))
if m5 != md5sum_str {
return nil, fmt.Errorf("md5sums do not match %s != %s (line %d)", m5, md5sum_str, line_no)
}
ti := emit_fastj_tile(tilepath, tilestep, span_len, s_tag, cur_seq, e_tag)
if tilevar == 0 {
allele_path[0] = append(allele_path[0], ti)
} else if tilevar == 1 {
allele_path[1] = append(allele_path[1], ti)
} else {
return nil, fmt.Errorf("invalid tile variant allele %d", tilevar)
}
}
first_tile = false
var pos int = 0
tileid, pos = simple_text_field(l[1:], "tileID")
if pos < 0 {
return nil, fmt.Errorf("no tileID found at line %d", line_no)
}
md5sum_str, pos = simple_text_field(l[1:], "md5sum")
if pos < 0 {
return nil, fmt.Errorf("no md5sum found at line %d", line_no)
}
span_len, pos = simple_int_field(l[1:], "seedTileLength")
if pos < 0 {
return nil, fmt.Errorf("no md5sum found at line %d", line_no)
}
s_tag, pos = simple_text_field(l[1:], "startTag")
if pos < 0 {
return nil, fmt.Errorf("no startTag found at line %d", line_no)
}
_ = s_tag
e_tag, pos = simple_text_field(l[1:], "endTag")
if pos < 0 {
return nil, fmt.Errorf("no endTag found at line %d", line_no)
}
_ = e_tag
start_tile_flag, pos = simple_bool_field(l[1:], "startTile")
if pos < 0 {
return nil, fmt.Errorf("no startTile found at line %d", line_no)
}
_ = start_tile_flag
end_tile_flag, pos = simple_bool_field(l[1:], "endTile")
if pos < 0 {
return nil, fmt.Errorf("no endTile found at line %d", line_no)
}
_ = end_tile_flag
tile_parts := strings.Split(tileid, ".")
if t, e := strconv.ParseInt(tile_parts[0], 16, 64); e == nil {
tilepath = int(t)
} else {
return nil, e
}
if t, e := strconv.ParseInt(tile_parts[2], 16, 64); e == nil {
tilestep = int(t)
} else {
return nil, e
}
if t, e := strconv.ParseInt(tile_parts[3], 16, 64); e == nil {
tilevar = int(t)
} else {
return nil, e
}
// Header parsed, go on
//
cur_seq = cur_seq[0:0]
continue
}
if first_tile {
return nil, fmt.Errorf("found body before header (line %d)", line_no)
}
cur_seq = append(cur_seq, l[:]...)
}
// store tile sequence
//
if !first_tile {
m5 := Md5sum2str(md5.Sum(cur_seq))
if m5 != md5sum_str {
return nil, fmt.Errorf("md5sums do not match %s != %s (line %d)", m5, md5sum_str, line_no)
}
ti := emit_fastj_tile(tilepath, tilestep, span_len, s_tag, cur_seq, e_tag)
if tilevar == 0 {
allele_path[0] = append(allele_path[0], ti)
} else if tilevar == 1 {
allele_path[1] = append(allele_path[1], ti)
} else {
return nil, fmt.Errorf("invalid tile variant allele %d", tilevar)
}
}
return allele_path, nil
}
func convert(gvcf_ain *autoio.AutoioHandle, ref_ain *simplestream.SimpleStream, aout *os.File, start_pos int64) error {
var e error
//start_pos := int64(0)
allele_num := 0
_ = allele_num
bufout := bufio.NewWriter(aout)
defer bufout.Flush()
cur_spos := int64(0)
// All co-ordinates are 0-ref.
// End is inclusive
//
for gvcf_ain.ReadScan() {
l := gvcf_ain.ReadText()
if len(l) == 0 || l[0] == '#' {
continue
}
gvcf_parts := strings.Split(l, "\t")
if len(gvcf_parts) < 9 {
return fmt.Errorf("not enough gvcf parts")
}
chrom := gvcf_parts[0]
_ = chrom
spos, e0 := strconv.ParseInt(gvcf_parts[1], 10, 64)
if e0 != nil {
return e0
}
spos--
id_str := gvcf_parts[2]
_ = id_str
ref_anch := gvcf_parts[3]
_ = ref_anch
alt_str := gvcf_parts[4]
_ = alt_str
qual := gvcf_parts[5]
_ = qual
filt := gvcf_parts[6]
_ = filt
info_str := gvcf_parts[7]
_ = info_str
fmt_str := gvcf_parts[8]
_ = fmt_str
samp_str := gvcf_parts[9]
_ = samp_str
// Check for END
//
epos := int64(-1)
info_parts := strings.Split(info_str, ";")
for i := 0; i < len(info_parts); i++ {
if strings.HasPrefix(info_parts[i], "END=") {
end_parts := strings.Split(info_parts[i], "=")
// End is inclusive
//
epos, e = strconv.ParseInt(end_parts[1], 10, 64)
epos--
if e != nil {
return e
}
break
}
}
ref_len := int64(len(ref_anch))
if epos >= 0 {
ref_len = epos - spos + 1
}
typ := "NOCALL"
if filt == "PASS" {
typ = "REF"
}
// Catch up to current position
//
if (cur_spos >= 0) && ((spos - cur_spos) > 0) {
//fmt.Printf("\nnocall catchup %d+%d\n", cur_spos, spos-cur_spos)
emit_nocall_ref(cur_spos, spos-cur_spos, ref_ain, bufout)
}
// Update previous end position
//
cur_spos = spos + ref_len
// Process current line
//
if typ == "NOCALL" {
//fmt.Printf("\nnocall ref %d+%d\n", spos, ref_len)
emit_nocall_ref(spos, ref_len, ref_ain, bufout)
continue
}
refseq, _, e := peel_ref(spos, ref_len, ref_ain)
if e != nil {
return e
}
gt_idx, er := get_field_index(fmt_str, "GT", ":")
if er != nil {
return er
}
samp_parts := strings.Split(samp_str, ":")
if len(samp_parts) <= gt_idx {
return fmt.Errorf(fmt.Sprintf("%s <-- NO GT FIELD", l))
}
gt_field := samp_parts[gt_idx]
gt_parts := []string{}
if strings.Index(gt_field, "/") != -1 {
gt_parts = strings.Split(gt_field, "/")
//fmt.Printf(" %s %s (un)\n", gt_parts[0], gt_parts[1])
} else if strings.Index(gt_field, "|") != -1 {
gt_parts = strings.Split(gt_field, "|")
//fmt.Printf(" %s %s (ph)\n", gt_parts[0], gt_parts[1])
} else {
gt_parts = append(gt_parts, gt_field)
//fmt.Printf(" %s\n", gt_field)
}
gt_allele_idx, e := convert_textvec(gt_parts)
//fmt.Printf(">> ref %s\n", refseq)
alt_fields := strings.Split(alt_str, ",")
for i := 0; i < len(gt_allele_idx); i++ {
if gt_allele_idx[i] == 0 {
//fmt.Printf("> alt%d %s\n", gt_allele_idx[i], refseq)
//aout.WriteString(refseq)
bufout.WriteString(refseq)
gCounter += len(refseq)
} else if (gt_allele_idx[i] - 1) < len(alt_fields) {
//fmt.Printf("> alt%d %s\n", gt_allele_idx[i],
//aout.WriteString(alt_fields[gt_allele_idx[i]-1])
bufout.WriteString(alt_fields[gt_allele_idx[i]-1])
gCounter += len(alt_fields[gt_allele_idx[i]-1])
} else {
return fmt.Errorf(fmt.Sprintf("%s <-- invalid GT field", l))
}
//DEBUG
// Only first allele for now
break
//DEBUG
}
//fmt.Printf("chrom %s, spos %d, epos %d\n", chrom, spos, epos)
}
//fmt.Printf("\n\ngCounter %d\n", gCounter)
return nil
}
func diff_to_interleave(ain *autoio.AutoioHandle) {
n_allele := 2
lfmod := 50
bp_count := 0
chrom := ""
pos := -1
first_pass := true
for ain.ReadScan() {
l := ain.ReadText()
if len(l) == 0 || l == "" {
continue
}
diff_parts := strings.Split(l, "\t")
chrom_s := diff_parts[0]
type_s := diff_parts[1]
st_s := diff_parts[2]
_ = st_s
en_s := diff_parts[3]
_ = en_s
field := diff_parts[4]
control_message := false
if chrom != chrom_s {
if !first_pass && !control_message {
fmt.Printf("\n")
}
fmt.Printf(">C{%s}", chrom_s)
chrom = chrom_s
control_message = true
}
_st, e := strconv.ParseUint(st_s, 10, 64)
if e == nil {
if pos != int(_st) {
if !first_pass && !control_message {
fmt.Printf("\n")
}
fmt.Printf(">P{%d}", _st)
pos = int(_st)
control_message = true
}
}
if control_message {
fmt.Printf("\n")
}
first_pass = false
if type_s == "ref" {
for i := 0; i < len(field); i++ {
for a := 0; a < n_allele; a++ {
fmt.Printf("%c", field[i])
bp_count++
if (lfmod > 0) && ((bp_count % lfmod) == 0) {
fmt.Printf("\n")
}
}
}
pos += len(field)
} else if type_s == "alt" || type_s == "nca" || type_s == "noc" {
field_parts := strings.Split(field, ";")
alt_parts := strings.Split(field_parts[0], "/")
if len(alt_parts) == 1 {
alt_parts = append(alt_parts, alt_parts[0])
}
refseq := field_parts[1]
mM := len(alt_parts[0])
if len(alt_parts[1]) > mM {
mM = len(alt_parts[1])
}
if len(refseq) > mM {
mM = len(refseq)
}
for i := 0; i < mM; i++ {
for a := 0; a < len(alt_parts); a++ {
if i < len(alt_parts[a]) {
if i < len(refseq) {
fmt.Printf("%c", pasta.SubMap[refseq[i]][alt_parts[a][i]])
} else {
fmt.Printf("%c", pasta.InsMap[alt_parts[a][i]])
}
} else if i < len(refseq) {
fmt.Printf("%c", pasta.DelMap[refseq[i]])
} else {
fmt.Printf(".")
}
bp_count++
if (lfmod > 0) && ((bp_count % lfmod) == 0) {
fmt.Printf("\n")
}
}
}
if refseq != "-" {
pos += len(refseq)
}
}
}
fmt.Printf("\n")
}