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cglf.go
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cglf.go
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package main
// cglf toolkit
import "fmt"
import "os"
import "runtime"
import "runtime/pprof"
import "log"
import _ "sort"
import "github.com/abeconnelly/autoio"
import "github.com/codegangsta/cli"
import "./dlug"
import "strings"
import "crypto/md5"
import "./twobit"
import "bytes"
import "compress/gzip"
import "io/ioutil"
import "strconv"
var VERSION_STR string = "0.1.0"
var gVerboseFlag bool
var gProfileFlag bool
var gProfileFile string = "cglf.pprof"
var gMemProfileFlag bool
var gMemProfileFile string = "cglf.mprof"
var g_debug bool = false
type TileLibEntry struct {
Seq string
Freq int
Span int
Diff []AltEntry
}
type AltEntry struct {
Start int
N int
Seq []byte
}
type AltOverflowRec struct {
BodySeqIndex uint64
Alt []AltEntry
}
type AltOverflow struct {
NAltCache uint64
N uint64
VariantId []uint64
Span []uint64
VariantType []uint64
VariantIndex []uint64
AuxBodySeq [][]byte
AltOverflowRec []AltOverflowRec
AltData [][]byte
}
func _diff_str(d []AltEntry) string {
s := []string{}
for i:=0; i<len(d); i++ {
s_ele := fmt.Sprintf("%x+%x{%s}", d[i].Start, d[i].N, d[i].Seq)
s = append(s, s_ele)
}
return strings.Join(s, ";")
}
func convert_cache_alt_entry(cachebuf []byte) ([]AltEntry, int) {
ael := []AltEntry{}
altnum := uint64(0)
n := 0
dn := 0
altnum,dn = dlug.ConvertUint64(cachebuf[n:])
n += dn
if altnum==0 { return nil,n }
var s,canon_len,alt_len uint64
for i:=uint64(0); i<altnum; i++ {
s,dn = dlug.ConvertUint64(cachebuf[n:])
n += dn
canon_len,dn = dlug.ConvertUint64(cachebuf[n:])
n += dn
alt_len,dn = dlug.ConvertUint64(cachebuf[n:])
n += dn
seq_2bit_byte_len := alt_len/4
if (alt_len%4)!=0 { seq_2bit_byte_len++ }
seq_2bit := cachebuf[n:n+int(seq_2bit_byte_len)]
n += int(seq_2bit_byte_len)
seq := make([]byte, alt_len)
twobit2seq_sn(seq, seq_2bit, 0, alt_len)
ael = append(ael, AltEntry{ Start:int(s), N:int(canon_len), Seq: seq })
}
return ael,n
}
func (alt_ovf *AltOverflow) init() {
alt_ovf.VariantId = make([]uint64, 0, 8)
alt_ovf.Span = make([]uint64, 0, 8)
alt_ovf.VariantType = make([]uint64, 0, 8)
alt_ovf.VariantIndex = make([]uint64, 0, 8)
alt_ovf.AuxBodySeq = make([][]byte, 0, 8)
alt_ovf.AltOverflowRec = []AltOverflowRec{}
alt_ovf.AltData = make([][]byte, 0, 8)
}
func peel_alt_overflow_bytes(buf []byte) (AltOverflow, uint64) {
alt_ovf := AltOverflow{}
alt_ovf.init()
var n int
n_alt_cache,dn := dlug.ConvertUint64(buf[n:])
n += dn
alt_ovf.NAltCache = n_alt_cache
var_num,dn := dlug.ConvertUint64(buf[n:])
n += dn
alt_ovf.N = var_num
if var_num==0 { return AltOverflow{}, uint64(n) }
variant_id_array := make([]uint64, 0, 8)
for i:=uint64(0); i<uint64(var_num); i++ {
vid,dn := dlug.ConvertUint64(buf[n:])
n+=dn
variant_id_array = append(variant_id_array, uint64(vid))
}
alt_ovf.VariantId = variant_id_array
span_array := make([]uint64, 0, 8)
for i:=uint64(0); i<uint64(var_num); i++ {
span,dn := dlug.ConvertUint64(buf[n:])
n+=dn
span_array = append(span_array, uint64(span))
}
alt_ovf.Span = span_array
variant_type_array := make([]uint64, 0, 8)
for i:=uint64(0); i<uint64(var_num); i++ {
typ,dn := dlug.ConvertUint64(buf[n:])
n+=dn
variant_type_array = append(variant_type_array, uint64(typ))
}
alt_ovf.VariantType = variant_type_array
variant_index_array := make([]uint64, 0, 8)
for i:=uint64(0); i<uint64(var_num); i++ {
idx,dn := dlug.ConvertUint64(buf[n:])
n+=dn
variant_index_array = append(variant_index_array, uint64(idx))
}
alt_ovf.VariantIndex = variant_index_array
alt_overflow_idx_to_variantid := make(map[uint64]uint64)
alt_overflow_idx_to_span := make(map[uint64]uint64)
for i:=uint64(0); i<uint64(var_num); i++ {
if variant_type_array[i]!=0 { continue }
alt_overflow_idx_to_variantid[ variant_index_array[i] ] = variant_id_array[i]
alt_overflow_idx_to_span[ variant_index_array[i] ] = variant_index_array[i]
}
alt_data_idx_to_variantid := make(map[uint64]uint64)
for i:=uint64(0); i<uint64(var_num); i++ {
if variant_type_array[i]!=1 { continue }
alt_data_idx_to_variantid[ variant_index_array[i] ] = variant_id_array[i]
}
aux_body_len := byte2uint64(buf[n:n+8])
n+=8
aux_body_seq_offset_bp := make([]uint64, aux_body_len)
for i:=uint64(0); i<aux_body_len; i++ {
aux_body_seq_offset_bp[i] = byte2uint64(buf[n:n+8])
n+=8
}
var aux_body_seq_twobit []byte
if aux_body_len>0 {
dbp := (aux_body_seq_offset_bp[aux_body_len-1]+3)/4
aux_body_seq_twobit = buf[n:n+int(dbp)]
n += int(dbp)
}
// Construct AuxBodySeq structure
//
aux_body_seq := make([][]byte, aux_body_len)
for i:=uint64(0); i<aux_body_len; i++ {
s_bp := uint64(0)
if i>0 { s_bp = aux_body_seq_offset_bp[i-1] }
e_bp := aux_body_seq_offset_bp[i]
aux_body_seq[i] = make([]byte, e_bp-s_bp)
twobit2seq_sn(aux_body_seq[i], aux_body_seq_twobit, s_bp, e_bp-s_bp)
}
alt_ovf.AuxBodySeq = aux_body_seq
/*
vid_idx := make(map[int]int)
for i:=0; i<len(alt_ovf.VariantId); i++ {
vid_idx[ int(alt_ovf.VariantId[i]) ] = i
}
*/
/*
//DEBUG
fmt.Printf("#VariantId.:")
for i:=0; i<len(alt_ovf.VariantId); i++ {
fmt.Printf(" %d", alt_ovf.VariantId[i])
}
fmt.Printf("\n")
fmt.Printf("#VariantTyp:")
for i:=0; i<len(alt_ovf.VariantType); i++ {
fmt.Printf(" %d", alt_ovf.VariantType[i])
}
fmt.Printf("\n")
fmt.Printf("#VariantInd:")
for i:=0; i<len(alt_ovf.VariantIndex); i++ {
fmt.Printf(" %d", alt_ovf.VariantIndex[i])
}
fmt.Printf("\n")
*/
altovf_vid_map := make(map[int]int)
for i:=0; i<len(alt_ovf.VariantId); i++ {
if alt_ovf.VariantType[i] != 0 { continue }
altovf_vid_map[ int(alt_ovf.VariantIndex[i]) ] = i
}
altdata_vid_map := make(map[int]int) ; _ = altdata_vid_map
for i:=0; i<len(alt_ovf.VariantId); i++ {
if alt_ovf.VariantType[i] != 1 { continue }
altdata_vid_map[ int(alt_ovf.VariantIndex[i]) ] = i
}
//
//----
alt_overflow_variant_len := byte2uint64(buf[n:n+8])
n+=8
alt_overflow_variant_rec_offset := make([]uint64, alt_overflow_variant_len)
for i:=uint64(0); i<alt_overflow_variant_len; i++ {
alt_overflow_variant_rec_offset[i] = byte2uint64(buf[n:n+8])
n+=8
}
alt_vid_map := make(map[int]string)
//experimental
//alt_ovf.AltOverflowRec = make([]AltOverflowRec, len(alt_ovf.VariantIndex))
alt_ovf.AltOverflowRec = make([]AltOverflowRec, len(alt_ovf.VariantId))
for ovf_ind:=uint64(0); ovf_ind<alt_overflow_variant_len; ovf_ind++ {
body_seq_index,dn := dlug.ConvertUint64(buf[n:]) ; _ = body_seq_index
n += dn
nalt,dn := dlug.ConvertUint64(buf[n:]) ; _ = nalt
n += dn
aor := AltOverflowRec{ BodySeqIndex: body_seq_index }
aor.Alt = []AltEntry{}
for alt_ind:=0; alt_ind<int(nalt); alt_ind++ {
start_bp,dn := dlug.ConvertUint64(buf[n:]) ; _ = start_bp
n += dn
canon_len_bp,dn := dlug.ConvertUint64(buf[n:]) ; _ = canon_len_bp
n += dn
alt_len_bp,dn := dlug.ConvertUint64(buf[n:]) ; _ = alt_len_bp
n += dn
dn = int((alt_len_bp+3)/4)
seq_twobit := buf[n:n+dn] ; _ = seq_twobit
n += dn
seq := make([]byte, alt_len_bp)
twobit2seq_sn(seq, seq_twobit, 0, alt_len_bp)
aor.Alt = append(aor.Alt, AltEntry{ Start: int(start_bp), N:int(canon_len_bp), Seq:seq } )
}
vid := alt_ovf.VariantId[ altovf_vid_map[int(ovf_ind)] ]
alt_ovf.AltOverflowRec[vid] = aor
}
alt_data_len := byte2uint64(buf[n:n+8])
n+=8
alt_data_offset := make([]uint64, alt_data_len, alt_data_len+1)
for i:=uint64(0); i<alt_data_len; i++ {
alt_data_offset[i] = byte2uint64(buf[n:n+8])
n+=8
}
alt_ind:=0 ; _ = alt_ind
if alt_data_len>0 {
dn = int(alt_data_offset[alt_data_len-1])
var bytebuf bytes.Buffer
bytebuf.Write(buf[n:n+dn])
gz_reader,e := gzip.NewReader(&bytebuf)
if e!=nil { panic(e) }
defer gz_reader.Close()
raw_bytes,e := ioutil.ReadAll(gz_reader)
if e!=nil { panic(e) }
twobit_reader := bytes.NewReader(raw_bytes)
tb,e := twobit.NewReader(twobit_reader)
if e!=nil { panic(e) }
nams := tb.Names()
for zz:=0; zz<len(nams);zz++ {
name_parts := strings.Split(nams[zz], ".")
if len(name_parts) < 4 { panic("...") }
step,e := strconv.ParseInt(name_parts[2], 16, 64)
varid,e := strconv.ParseInt(name_parts[3], 16, 64)
if e!=nil { panic("...") }
_ = step
bb,e := tb.Read(nams[zz])
if e!=nil { panic(e) }
alt_vid_map[int(varid)] = string(bb)
aor := AltOverflowRec{ BodySeqIndex: 0 }
aor.Alt = []AltEntry{}
aor.Alt = append(aor.Alt, AltEntry{ Start:0, N:-1, Seq: bb })
alt_ovf.AltOverflowRec[varid] = aor
}
n+=dn
}
return alt_ovf, uint64(n)
}
func exit_error(msg string, err error ) {
log.Fatal( fmt.Sprintf("%s, got %v", msg, err) )
}
type CGLFPath struct {
Path uint64
NStep uint64
TagLenBP uint64
TagSeqTwoBit []byte
BodySeqLenBP uint64
BodySeqOffsetBP []uint64
BodySeqTwoBit []byte
Span []byte
SpanOverflowLen uint64
SpanOverflow []uint64
AltCache []byte
AltOverflowOffset []uint64
AltOverflow []byte
}
type CGLF struct {
Magic string
VersionMajor uint32
VersionMinor uint32
VersionPatch uint32
NPath uint64
AltStride uint64
TagStride uint64
PathOffset []uint64
Path []CGLFPath
}
type CGLFPath_ struct {
Path uint64
NStep uint64
TagLenBP uint64
TagSeqTwoBit []byte
BodySeqLenBP uint64
BodySeqOffsetBP []uint64
BodySeqTwoBit []byte
Span []byte
SpanOverflowLen uint64
SpanOverflow []uint64
AltCache []byte
AltOverflowOffset []uint64
AltOverflow []byte
}
var g_tile_lib map[int]map[int][]TileLibEntry
var g_body_seq map[int]string
var g_tag_seq map[int]string
var g_cglf CGLF
type ByAltEntry []AltEntry
func (f ByAltEntry) Len() int { return len(f) }
func (f ByAltEntry) Less(i,j int) bool { return f[i].Start < f[j].Start }
func (f ByAltEntry) Swap(i,j int) { f[i],f[j] = f[j],f[i] }
func construct_body_seq(base_seq string, alt []AltEntry) string {
//sort.Sort(ByAltEntry(alt))
ref_pos := 0
alt_seq := make([]byte, 0, len(base_seq))
for i:=0; i<len(alt); i++ {
if alt[i].Start > ref_pos {
n:=len(base_seq)
if (ref_pos >= n) || (alt[i].Start>n) {
es := fmt.Sprintf("nope: ref_pos %d, alt[%d].Start %d, len(base_seq) %d", ref_pos, i, alt[i].Start, n)
panic(es)
}
alt_seq = append(alt_seq, base_seq[ref_pos:alt[i].Start]...)
ref_pos = alt[i].Start
}
if len(alt[i].Seq)>0 {
alt_seq = append(alt_seq, alt[i].Seq...)
}
ref_pos += alt[i].N
}
if ref_pos < len(base_seq) {
alt_seq = append(alt_seq, base_seq[ref_pos:]...)
}
return string(alt_seq)
}
func populate_tile_lib_sequences() {
for path,_ := range g_tile_lib {
body_seq := g_body_seq
tag_seq := g_tag_seq
for step,_ := range g_tile_lib[path] {
var base_seq string
if step==0 {
base_seq = fmt.Sprintf("%s%s", body_seq[step], tag_seq[step])
} else if step==len(tag_seq) {
base_seq = fmt.Sprintf("%s%s", tag_seq[step-1], body_seq[step])
} else {
if step<1 || step >= len(tag_seq) {
es := fmt.Sprintf(">>>>> step %d, len(tag_seq) %d\n", step, len(tag_seq))
fmt.Printf(es)
panic(es)
}
base_seq = fmt.Sprintf("%s%s%s", tag_seq[step-1], body_seq[step], tag_seq[step])
}
for var_idx := 0 ; var_idx < len(g_tile_lib[path][step]); var_idx++ {
var s string
if var_idx > 0 {
//DEBUG
//fmt.Printf("#(A) %x.%x\n", path, step)
s = construct_body_seq(base_seq, g_tile_lib[path][step][var_idx].Diff)
} else {
s = base_seq
}
z := g_tile_lib[path][step][var_idx]
z.Seq = s
g_tile_lib[path][step][var_idx] = z
}
}
}
}
func load_cglf_quick(fp *os.File) {
var n int
var e error
buf := make([]byte, 1024)
magic := "{\"cglf\":\"bin\""
for i:=0; i<len(magic); i++ {
n,e := fp.Read(buf[0:1])
if n!=1 || e!=nil {
log.Fatal("NOT a CGLF file")
}
if buf[0] != magic[i] {
log.Fatal("NOT a CGLF file")
}
}
g_cglf.Magic = magic
n,e = fp.Read(buf[0:4])
if n<4 || e!=nil { exit_error("ERROR reading major version number", e) }
ver_maj := byte2uint32(buf[0:4])
g_cglf.VersionMajor = ver_maj
n,e = fp.Read(buf[0:4])
if n<4 || e!=nil { exit_error("ERROR reading minor version number", e) }
ver_min := byte2uint32(buf[0:4])
g_cglf.VersionMinor = ver_min
n,e = fp.Read(buf[0:4])
if n<4 || e!=nil { exit_error("ERROR reading patch version number", e) }
ver_pat := byte2uint32(buf[0:4])
g_cglf.VersionPatch = ver_pat
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { exit_error("ERROR reading number of paths", e) }
npath := byte2uint64(buf[0:8])
g_cglf.NPath = npath
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { exit_error("ERROR reading alt stride", e) }
altstride := byte2uint64(buf[0:8])
g_cglf.AltStride = altstride
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { exit_error("ERROR reading tag stride", e) }
tagstride := byte2uint64(buf[0:8])
g_cglf.TagStride = tagstride
path_offset := make([]uint64, npath)
for i:=uint64(0); i<npath; i++ {
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { log.Fatal( fmt.Sprintf("ERROR reading path %d length, %v", i, e) ) }
path_offset[i] = byte2uint64(buf[0:8])
}
//DEBUG
//fmt.Printf("# >> npath %d\n", npath)
g_cglf.PathOffset = path_offset
g_cglf.Path = make([]CGLFPath, g_cglf.NPath)
for path_idx:=uint64(0) ; path_idx<npath; path_idx++ {
_path_idx := int(path_idx)
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { fmt.Printf("%d %v\n", n, e) }
path := byte2uint64(buf[0:8])
g_cglf.Path[_path_idx].Path = path
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { fmt.Printf("%d %v\n", n, e) }
nstep := byte2uint64(buf[0:8])
g_cglf.Path[_path_idx].NStep = nstep
//-----------
// tag
//-----------
//DEBUG
//fmt.Printf("#>>> path %x, tagstride, %d, nstep %d\n", path, tagstride, nstep)
ntile := nstep
taglen_bp := (ntile-1)*tagstride
tag_seq_2bit := make([]byte, ((taglen_bp+3)/4))
n,e = fp.Read(tag_seq_2bit)
if n!=len(tag_seq_2bit) || e!=nil { log.Fatal(e) }
g_cglf.Path[_path_idx].TagLenBP = taglen_bp
g_cglf.Path[_path_idx].TagSeqTwoBit = tag_seq_2bit
//-----------
// tag
//-----------
//-----------
// seq
//-----------
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { fmt.Printf("%d %v\n", n, e) }
seq_len_bp := byte2uint64(buf[0:8])
seq_byte_len := ((seq_len_bp+3)/4)
// Faster to read the whole byte array then convert in memory?
//
seq_bp_offset := make([]uint64, ntile)
tbuf := make([]byte, ntile*8)
n,e = fp.Read(tbuf)
if n!=len(tbuf) || e!=nil { log.Fatal(fmt.Sprintf("ERROR reading seq offset (len %d) on path[%d] %d, got %v", ntile, path_idx, path, e)) }
max_body_byte_len := uint64(0)
for ii:=uint64(0); ii<ntile; ii++ {
seq_bp_offset[ii] = byte2uint64(tbuf[8*ii:8*(ii+1)])
if (ii>0) && ((seq_bp_offset[ii]-seq_bp_offset[ii-1]) > max_body_byte_len) {
max_body_byte_len = seq_bp_offset[ii]-seq_bp_offset[ii-1]
}
}
seq_2bit := make([]byte, seq_byte_len)
n,e = fp.Read(seq_2bit)
if n!=len(seq_2bit) || e!=nil { log.Fatal(fmt.Sprintf("ERROR reading seq (len %d) on path[%d] %d, got %v", seq_len_bp, path_idx, path, e)) }
g_cglf.Path[_path_idx].BodySeqLenBP = seq_len_bp
g_cglf.Path[_path_idx].BodySeqTwoBit = seq_2bit
g_cglf.Path[_path_idx].BodySeqOffsetBP = seq_bp_offset
//-----------
// seq
//-----------
//-----------
// span
//-----------
span_byte := make([]byte, ntile)
n,e = fp.Read(span_byte)
if n!=len(span_byte) || e!=nil { log.Fatal(fmt.Sprintf("ERROR reading span (len %d) on path[%d] %d, got %v", len(span_byte), path_idx, path, e)) }
n,e = fp.Read(buf[0:8])
if n!=8 || e!=nil { log.Fatal(fmt.Sprintf("ERROR reading span overflow length on path[%d] %d, got %v", path_idx, path, e)) }
span_ovf_len := byte2uint64(buf[0:8])
span_ovf := []uint64{}
if span_ovf_len > 0 {
span_ovf = make([]uint64, 2*span_ovf_len)
tbuf := make([]byte, 16*span_ovf_len)
n,e = fp.Read(tbuf)
if n!=len(tbuf) || e!=nil {
log.Fatal(fmt.Sprintf("ERROR reading span overflow (len %d) on path[%d] %d, got %v", span_ovf_len, path_idx, path, e))
}
for ii:=uint64(0); ii<span_ovf_len; ii++ {
span_ovf[2*ii] = byte2uint64(tbuf[16*ii :16*ii+ 8])
span_ovf[2*ii+1] = byte2uint64(tbuf[16*ii+8:16*ii+16])
}
}
g_cglf.Path[_path_idx].Span = span_byte
g_cglf.Path[_path_idx].SpanOverflowLen = span_ovf_len
g_cglf.Path[_path_idx].SpanOverflow = span_ovf
//-----------
// span
//-----------
//-----------
// AltCache
//-----------
alt_cache_byte := make([]byte, altstride*ntile)
n,e = fp.Read(alt_cache_byte)
if n!=len(alt_cache_byte) || e!=nil {
log.Fatal(fmt.Sprintf("ERROR reading alt cache (expected %d, got %d) path[%d] %d, got %v", len(alt_cache_byte), n, path_idx, path, e))
}
g_cglf.Path[_path_idx].AltCache = alt_cache_byte
//-----------
// AltCache
//-----------
//-----------
// AltOverflowOffset
//-----------
alt_overflow_offset_bytes := make([]byte, 8*ntile)
n,e = fp.Read(alt_overflow_offset_bytes)
if n!=len(alt_overflow_offset_bytes) || e!=nil {
log.Fatal(fmt.Sprintf("ERROR reading alt overflow offset (expected %d, got %d) path[%d] %d, got %v",
len(alt_overflow_offset_bytes), n, path_idx, path, e))
}
alt_overflow_offset := make([]uint64, ntile)
for ii:=uint64(0); ii<ntile; ii++ {
alt_overflow_offset[ii] = byte2uint64(alt_overflow_offset_bytes[8*ii:8*(ii+1)])
}
alt_overflow_byte_len := alt_overflow_offset[ntile-1]
alt_overflow_bytes := make([]byte, alt_overflow_byte_len)
n,e = fp.Read(alt_overflow_bytes)
if n!=len(alt_overflow_bytes) || e!=nil {
log.Fatal(fmt.Sprintf("ERROR reading alt overflow (expected %d, got %d) path[%d] %d, got %v",
len(alt_overflow_bytes), n, path_idx, path, e))
}
g_cglf.Path[_path_idx].AltOverflowOffset = alt_overflow_offset
g_cglf.Path[_path_idx].AltOverflow = alt_overflow_bytes
//-----------
// AltOverflowOffset
//-----------
}
}
func load_cglf(fp *os.File) {
var n int
var e error
buf := make([]byte, 1024)
magic := "{\"cglf\":\"bin\""
for i:=0; i<len(magic); i++ {
n,e := fp.Read(buf[0:1])
if n!=1 || e!=nil {
log.Fatal("NOT a CGLF file")
}
if buf[0] != magic[i] {
log.Fatal("NOT a CGLF file")
}
}
g_cglf.Magic = magic
n,e = fp.Read(buf[0:4])
if n<4 || e!=nil { exit_error("ERROR reading major version number", e) }
ver_maj := byte2uint32(buf[0:4])
g_cglf.VersionMajor = ver_maj
n,e = fp.Read(buf[0:4])
if n<4 || e!=nil { exit_error("ERROR reading minor version number", e) }
ver_min := byte2uint32(buf[0:4])
g_cglf.VersionMinor = ver_min
n,e = fp.Read(buf[0:4])
if n<4 || e!=nil { exit_error("ERROR reading patch version number", e) }
ver_pat := byte2uint32(buf[0:4])
g_cglf.VersionPatch = ver_pat
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { exit_error("ERROR reading number of paths", e) }
npath := byte2uint64(buf[0:8])
g_cglf.NPath = npath
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { exit_error("ERROR reading alt stride", e) }
altstride := byte2uint64(buf[0:8])
g_cglf.AltStride = altstride
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { exit_error("ERROR reading tag stride", e) }
tagstride := byte2uint64(buf[0:8])
g_cglf.TagStride = tagstride
path_offset := make([]uint64, npath)
for i:=uint64(0); i<npath; i++ {
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { log.Fatal( fmt.Sprintf("ERROR reading path %d length, %v", i, e) ) }
path_offset[i] = byte2uint64(buf[0:8])
}
g_cglf.PathOffset = path_offset
g_cglf.Path = make([]CGLFPath, g_cglf.NPath)
tag_seq := make([]byte, tagstride)
g_tile_lib = make(map[int]map[int][]TileLibEntry)
for path_idx:=uint64(0) ; path_idx<npath; path_idx++ {
_path_idx := int(path_idx)
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { fmt.Printf("%d %v\n", n, e) }
path := byte2uint64(buf[0:8])
g_cglf.Path[_path_idx].Path = path
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { fmt.Printf("%d %v\n", n, e) }
nstep := byte2uint64(buf[0:8])
g_cglf.Path[_path_idx].NStep = nstep
//-----------
// tag
//-----------
ntile := nstep
taglen_bp := (ntile-1)*tagstride
tag_seq_2bit := make([]byte, ((taglen_bp+3)/4))
n,e = fp.Read(tag_seq_2bit)
if n!=len(tag_seq_2bit) || e!=nil { log.Fatal(e) }
g_cglf.Path[_path_idx].TagLenBP = taglen_bp
g_cglf.Path[_path_idx].TagSeqTwoBit = tag_seq_2bit
// we can figure out the number of tiles from the tag lengths
// We don't have a beginning an end tag, so:
// (number of tiles) = (number of tags) + 1
//
g_tag_seq = make(map[int]string)
tag_seq_map := make(map[int]string)
for ii:=uint64(0); ii<(ntile-1); ii++ {
twobit2seq(tag_seq, tag_seq_2bit[6*ii:6*(ii+1)])
g_tag_seq[int(ii)] = string(tag_seq)
tag_seq_map[int(ii)] = string(tag_seq)
}
//-----------
// tag
//-----------
//-----------
// seq
//-----------
n,e = fp.Read(buf[0:8])
if n<8 || e!=nil { fmt.Printf("%d %v\n", n, e) }
seq_len_bp := byte2uint64(buf[0:8])
seq_byte_len := ((seq_len_bp+3)/4)
// Faster to read the whole byte array then convert in memory?
//
seq_bp_offset := make([]uint64, ntile)
tbuf := make([]byte, ntile*8)
n,e = fp.Read(tbuf)
if n!=len(tbuf) || e!=nil { log.Fatal(fmt.Sprintf("ERROR reading seq offset (len %d) on path[%d] %d, got %v", ntile, path_idx, path, e)) }
max_body_byte_len := uint64(0)
for ii:=uint64(0); ii<ntile; ii++ {
seq_bp_offset[ii] = byte2uint64(tbuf[8*ii:8*(ii+1)])
if (ii>0) && ((seq_bp_offset[ii]-seq_bp_offset[ii-1]) > max_body_byte_len) {
max_body_byte_len = seq_bp_offset[ii]-seq_bp_offset[ii-1]
}
}
seq_2bit := make([]byte, seq_byte_len)
n,e = fp.Read(seq_2bit)
if n!=len(seq_2bit) || e!=nil { log.Fatal(fmt.Sprintf("ERROR reading seq (len %d) on path[%d] %d, got %v", seq_len_bp, path_idx, path, e)) }
g_body_seq = make(map[int]string)
canon_seq_map := make(map[int]string)
last_bp_offset := uint64(0)
for ii:=uint64(0); ii<ntile; ii++ {
ds := seq_bp_offset[ii]-last_bp_offset
body_seq := make([]byte, ds)
twobit2seq_sn(body_seq, seq_2bit, last_bp_offset, ds)
last_bp_offset = seq_bp_offset[ii]
g_body_seq[int(ii)] = string(body_seq)
}
g_cglf.Path[_path_idx].BodySeqLenBP = seq_len_bp
g_cglf.Path[_path_idx].BodySeqTwoBit = seq_2bit
g_cglf.Path[_path_idx].BodySeqOffsetBP = seq_bp_offset
//-----------
// seq
//-----------
//-----------
// span
//-----------
g_span := make([]uint64, ntile)
span_byte := make([]byte, ntile)
n,e = fp.Read(span_byte)
if n!=len(span_byte) || e!=nil { log.Fatal(fmt.Sprintf("ERROR reading span (len %d) on path[%d] %d, got %v", len(span_byte), path_idx, path, e)) }
n,e = fp.Read(buf[0:8])
if n!=8 || e!=nil { log.Fatal(fmt.Sprintf("ERROR reading span overflow length on path[%d] %d, got %v", path_idx, path, e)) }
span_ovf_len := byte2uint64(buf[0:8])
span_ovf := []uint64{}
if span_ovf_len > 0 {
span_ovf = make([]uint64, 2*span_ovf_len)
tbuf := make([]byte, 16*span_ovf_len)
n,e = fp.Read(tbuf)
if n!=len(tbuf) || e!=nil {
log.Fatal(fmt.Sprintf("ERROR reading span overflow (len %d) on path[%d] %d, got %v", span_ovf_len, path_idx, path, e))
}