func (ctx *LanternContext) LoadCGFIntermediate() {
for i := 0; i < len(ctx.CGFBytes); i++ {
hdri, _ := cgf.HeaderIntermediateFromBytes(ctx.CGFBytes[i])
ctx.CGFi = append(ctx.CGFi, hdri)
m0, _ := cgf.PathIntermediateFromBytes(hdri.PathBytes[0x247])
ctx.CGFPathi = append(ctx.CGFPathi, m0)
m1, _ := cgf.PathIntermediateFromBytes(hdri.PathBytes[0x2c5])
ctx.CGFPathi = append(ctx.CGFPathi, m1)
}
}
func (ctx *LanternContext) CGFSimpleStats_() {
n := len(ctx.CGFBytes)
paths := []int{0x247, 0x2c5}
fmt.Printf("start\n")
for ii := 0; ii < len(paths); ii++ {
path := paths[ii]
for i := 0; i < n; i++ {
hdri, _ := cgf.HeaderIntermediateFromBytes(ctx.CGFBytes[i])
path_bytes := hdri.PathBytes[path]
pathi, _ := cgf.PathIntermediateFromBytes(path_bytes)
count := 0
for i := 0; i < len(pathi.VecUint64); i++ {
u := (pathi.VecUint64[i] >> 32)
for j := uint32(0); j < 32; j++ {
if (u & (1 << j)) > 0 {
count++
}
}
}
c_count := len(pathi.VecUint64)*32 - count
_ = c_count
//fmt.Printf("[%d] path %x canon: %d/%d, (non-cacnon %d/%d)\n", i, path, c_count, len(pathi.VecUint64)*32, count, len(pathi.VecUint64)*32)
}
}
fmt.Printf("end\n")
pprof.StartCPUProfile(g_pprof)
pprof.StopCPUProfile()
os.Exit(0)
}
func _main(c *cli.Context) {
gShowKnotNocallInfoFlag = !c.Bool("hide-knot-low-quality")
inp_slice := c.StringSlice("input")
cglf_lib_location := c.String("cglf")
action := c.String("action")
if action == "debug" {
//debug_read(c.String("cgf"))
cgf.DebugRead(c.String("cgf"))
return
} else if action == "headercheck" {
//header_bytes := cgf_default_header_bytes()
header_bytes := cgf.CGFDefaultHeaderBytes()
//hdri,dn := headerintermediate_from_bytes(header_bytes) ; _ = dn
hdri, dn := cgf.HeaderIntermediateFromBytes(header_bytes)
_ = dn
//hdri_bytes := bytes_from_headerintermediate(hdri)
hdri_bytes := cgf.BytesFromHeaderIntermediate(hdri)
//hdri1,dn2 := headerintermediate_from_bytes(hdri_bytes) ; _ = dn2
hdri1, dn2 := cgf.HeaderIntermediateFromBytes(hdri_bytes)
_ = dn2
//err := headerintermediate_cmp(hdri, hdri1)
err := cgf.HeaderIntermediateCmp(hdri, hdri1)
if err != nil {
log.Fatal(err)
}
return
} else if action == "header" {
ocgf := c.String("output")
//header_bytes := cgf_default_header_bytes()
header_bytes := cgf.CGFDefaultHeaderBytes()
f, err := os.Create(ocgf)
if err != nil {
log.Fatal(err)
}
f.Write(header_bytes)
f.Sync()
f.Close()
return
} else if action == "knot" {
cglf_path := c.String("cglf")
if len(cglf_path) == 0 {
fmt.Fprintf(os.Stderr, "Provide CGLF\n")
cli.ShowAppHelp(c)
os.Exit(1)
}
cgf_bytes, e := ioutil.ReadFile(c.String("cgf"))
if e != nil {
log.Fatal(e)
}
//hdri,dn := headerintermediate_from_bytes(cgf_bytes[:])
hdri, dn := cgf.HeaderIntermediateFromBytes(cgf_bytes[:])
_ = hdri
_ = dn
//path,ver,step,e := parse_tilepos(c.String("tilepos"))
path, ver, step, e := cgf.ParseTilepos(c.String("tilepos"))
if e != nil {
log.Fatal(e)
}
if path < 0 {
log.Fatal("path must be positive")
}
if step < 0 {
log.Fatal("step must be positive")
}
//if path >= len(hdri.step_per_path) { log.Fatal("path out of range (max ", len(hdri.step_per_path), " paths)") }
//if step>= hdri.step_per_path[path] { log.Fatal("step out of range (max ", hdri.step_per_path[path], " steps)") }
if path >= len(hdri.StepPerPath) {
log.Fatal("path out of range (max ", len(hdri.StepPerPath), " paths)")
}
if step >= hdri.StepPerPath[path] {
log.Fatal("step out of range (max ", hdri.StepPerPath[path], " steps)")
}
//pathi,_ := pathintermediate_from_bytes(hdri.path_bytes[path])
pathi, _ := cgf.PathIntermediateFromBytes(hdri.PathBytes[path])
knot := cgf.GetKnot(hdri.TileMap, pathi, step)
if knot == nil {
fmt.Printf("spanning tile?\n")
} else {
for i := 0; i < len(knot); i++ {
phase_str := "A"
if i == 1 {
phase_str = "B"
}
for j := 0; j < len(knot[i]); j++ {
fmt.Printf("%s %04x.%02x.%04x.%03x+%x",
phase_str,
path, ver,
knot[i][j].Step,
knot[i][j].VarId,
knot[i][j].Span)
seq := cgf.CGLFGetLibSeq(uint64(path),
uint64(knot[i][j].Step),
uint64(knot[i][j].VarId),
uint64(knot[i][j].Span),
cglf_path)
if len(knot[i][j].NocallStartLen) > 0 {
fmt.Printf("*{")
for p := 0; p < len(knot[i][j].NocallStartLen); p += 2 {
if p > 0 {
fmt.Printf(";")
}
fmt.Printf("%d+%d",
knot[i][j].NocallStartLen[p],
knot[i][j].NocallStartLen[p+1])
}
fmt.Printf("}")
//noc_seq := fill_noc_seq(seq, knot[i][j].NocallStartLen)
noc_seq := cgf.FillNocSeq(seq, knot[i][j].NocallStartLen)
noc_m5str := cgf.Md5sum2str(md5.Sum([]byte(noc_seq)))
fmt.Printf(" %s\n%s\n", noc_m5str, noc_seq)
} else {
m5str := cgf.Md5sum2str(md5.Sum([]byte(seq)))
fmt.Printf(" %s\n%s\n", m5str, seq)
}
}
}
}
return
} else if action == "fastj" {
tilepos_str := c.String("tilepos")
if len(tilepos_str) == 0 {
log.Fatal("missing tilepos")
}
if use_SGLF {
_sglf, e := cglf.LoadGenomeLibraryCSV(c.String("sglf"))
if e != nil {
log.Fatal(e)
}
for i := 0; i < len(inp_slice); i++ {
//e = print_tile_sglf(inp_slice[i], tilepos_str, sglf)
e = cgf.PrintTileSGLF(inp_slice[i], tilepos_str, _sglf)
if e != nil {
log.Fatal(e)
}
}
} else {
if len(c.String("cgf")) != 0 {
inp_slice = append(inp_slice, c.String("cgf"))
}
for i := 0; i < len(inp_slice); i++ {
//e := print_tile_cglf(inp_slice[i], tilepos_str, cglf_lib_location)
e := cgf.PrintTileCGLF(inp_slice[i], tilepos_str, cglf_lib_location)
if e != nil {
log.Fatal(e)
}
}
}
return
} else if action == "fastj-range" {
tilepos_str := c.String("tilepos")
pos_parts := strings.Split(tilepos_str, ".")
if (len(pos_parts) != 2) && (len(pos_parts) != 3) {
fmt.Fprintf(os.Stderr, "Invalid tilepos\n")
cli.ShowAppHelp(c)
os.Exit(1)
}
path_range, e := parseIntOption(pos_parts[0], 16)
if e != nil {
fmt.Fprintf(os.Stderr, "Invalid path in tilepos: %v\n", e)
cli.ShowAppHelp(c)
os.Exit(1)
}
pp := 1
if len(pos_parts) == 3 {
pp = 2
}
step_range, e := parseIntOption(pos_parts[pp], 16)
if e != nil {
fmt.Fprintf(os.Stderr, "Invalid step in tilepos: %v\n", e)
cli.ShowAppHelp(c)
os.Exit(1)
}
if len(tilepos_str) == 0 {
log.Fatal("missing tilepos")
}
if len(c.String("sglf")) > 0 {
use_SGLF = true
}
if use_SGLF {
_sglf, e := cglf.LoadGenomeLibraryCSV(c.String("sglf"))
_ = _sglf
if e != nil {
log.Fatal(e)
}
if len(c.String("cgf")) != 0 {
inp_slice = append(inp_slice, c.String("cgf"))
}
for i := 0; i < len(inp_slice); i++ {
cgf_bytes, e := ioutil.ReadFile(inp_slice[i])
if e != nil {
log.Fatal(e)
}
path := path_range[0][0]
//hdri,_ := headerintermediate_from_bytes(cgf_bytes) ; _ = hdri
//pathi,_ := pathintermediate_from_bytes(hdri.PathBytes[path]) ; _ = pathi
hdri, _ := cgf.HeaderIntermediateFromBytes(cgf_bytes)
_ = hdri
pathi, _ := cgf.PathIntermediateFromBytes(hdri.PathBytes[path])
_ = pathi
//hdri,dn := headerintermediate_from_bytes(cgf_bytes)
hdri, dn := cgf.HeaderIntermediateFromBytes(cgf_bytes)
if dn < 0 {
log.Fatal("could not construct header from bytes")
}
//patho,dn := pathintermediate_from_bytes(hdri.PathBytes[path])
patho, dn := cgf.PathIntermediateFromBytes(hdri.PathBytes[path])
if dn < 0 {
log.Fatal("could not construct path")
}
tilemap_bytes, _ := cgf.CGFTilemapBytes(cgf_bytes)
//tilemap := unpack_tilemap(tilemap_bytes)
tilemap := cgf.UnpackTileMap(tilemap_bytes)
for step_idx := 0; step_idx < len(step_range); step_idx++ {
if step_range[step_idx][1] == -1 {
//step_range[step_idx][1] = int64(hdri.step_per_path[path])
step_range[step_idx][1] = int64(hdri.StepPerPath[path])
}
}
for stepr_idx := 0; stepr_idx < len(step_range); stepr_idx++ {
for step := step_range[stepr_idx][0]; step < step_range[stepr_idx][1]; step++ {
//knot := GetKnot(tilemap, patho, int(step))
//print_knot_fastj_sglf(knot, _sglf, uint64(path), 0, hdri)
knot := cgf.GetKnot(tilemap, patho, int(step))
cgf.PrintKnotFastjSGLF(knot, _sglf, uint64(path), 0, hdri)
}
}
}
return
} else {
if len(c.String("cgf")) != 0 {
inp_slice = append(inp_slice, c.String("cgf"))
}
for i := 0; i < len(inp_slice); i++ {
cgf_bytes, e := ioutil.ReadFile(inp_slice[i])
if e != nil {
log.Fatal(e)
}
path := path_range[0][0]
_sglf := cglf.SGLF{}
//populate_sglf_from_cglf(c.String("cglf"), &_sglf, uint64(path))
cgf.PopulateSGLFFromCGLF(c.String("cglf"), &_sglf, uint64(path))
os.Exit(0)
//hdri,_ := headerintermediate_from_bytes(cgf_bytes) ; _ = hdri
//pathi,_ := pathintermediate_from_bytes(hdri.PathBytes[path]) ; _ = pathi
hdri, _ := cgf.HeaderIntermediateFromBytes(cgf_bytes)
_ = hdri
pathi, _ := cgf.PathIntermediateFromBytes(hdri.PathBytes[path])
_ = pathi
//hdri,dn := headerintermediate_from_bytes(cgf_bytes)
hdri, dn := cgf.HeaderIntermediateFromBytes(cgf_bytes)
if dn < 0 {
log.Fatal("could not construct header from bytes")
}
//patho,dn := pathintermediate_from_bytes(hdri.PathBytes[path])
patho, dn := cgf.PathIntermediateFromBytes(hdri.PathBytes[path])
if dn < 0 {
log.Fatal("could not construct path")
}
tilemap_bytes, _ := cgf.CGFTilemapBytes(cgf_bytes)
//tilemap := unpack_tilemap(tilemap_bytes)
tilemap := cgf.UnpackTileMap(tilemap_bytes)
for step_idx := 0; step_idx < len(step_range); step_idx++ {
if step_range[step_idx][1] == -1 {
//step_range[step_idx][1] = int64(hdri.step_per_path[path])
step_range[step_idx][1] = int64(hdri.StepPerPath[path])
}
}
for stepr_idx := 0; stepr_idx < len(step_range); stepr_idx++ {
for step := step_range[stepr_idx][0]; step < step_range[stepr_idx][1]; step++ {
//knot := GetKnot(tilemap, patho, int(step))
//print_knot_fastj_sglf(knot, _sglf, uint64(path), 0, hdri)
knot := cgf.GetKnot(tilemap, patho, int(step))
cgf.PrintKnotFastjSGLF(knot, _sglf, uint64(path), 0, hdri)
}
}
}
}
return
} else if action == "knot-z" {
cgf_bytes, e := ioutil.ReadFile(c.String("cgf"))
_ = cgf_bytes
if e != nil {
log.Fatal(e)
}
path, ver, step, e := cgf.ParseTilepos(c.String("tilepos"))
_ = path
_ = ver
_ = step
if e != nil {
log.Fatal(e)
}
if path < 0 {
log.Fatal("path must be positive")
}
if step < 0 {
log.Fatal("step must be positive")
}
fmt.Printf("not implemented\n")
return
} else if action == "knot-2" {
cgf_bytes, e := ioutil.ReadFile(c.String("cgf"))
if e != nil {
log.Fatal(e)
}
//hdri,dn := headerintermediate_from_bytes(cgf_bytes[:])
hdri, dn := cgf.HeaderIntermediateFromBytes(cgf_bytes[:])
_ = hdri
_ = dn
//path,ver,step,e := parse_tilepos(c.String("tilepos"))
path, ver, step, e := cgf.ParseTilepos(c.String("tilepos"))
if e != nil {
log.Fatal(e)
}
if path < 0 {
log.Fatal("path must be positive")
}
if step < 0 {
log.Fatal("step must be positive")
}
//if path >= len(hdri.step_per_path) { log.Fatal("path out of range (max ", len(hdri.step_per_path), " paths)") }
//if step>= hdri.step_per_path[path] { log.Fatal("step out of range (max ", hdri.step_per_path[path], " steps)") }
if path >= len(hdri.StepPerPath) {
log.Fatal("path out of range (max ", len(hdri.StepPerPath), " paths)")
}
if step >= hdri.StepPerPath[path] {
log.Fatal("step out of range (max ", hdri.StepPerPath[path], " steps)")
}
//pathi,_ := pathintermediate_from_bytes(hdri.PathBytes[path])
pathi, _ := cgf.PathIntermediateFromBytes(hdri.PathBytes[path])
//knot := GetKnot(hdri.tilemap, pathi, step)
knot := cgf.GetKnot(hdri.TileMap, pathi, step)
if knot == nil {
fmt.Printf("spanning tile?")
} else {
for i := 0; i < len(knot); i++ {
for j := 0; j < len(knot[i]); j++ {
if j > 0 {
fmt.Printf(" ")
}
fmt.Printf("%04x.%02x.%04x.%03x+%x",
path, ver,
knot[i][j].Step,
knot[i][j].VarId,
knot[i][j].Span)
if gShowKnotNocallInfoFlag {
if len(knot[i][j].NocallStartLen) > 0 {
fmt.Printf("*{")
for p := 0; p < len(knot[i][j].NocallStartLen); p += 2 {
if p > 0 {
fmt.Printf(";")
}
fmt.Printf("%d+%d",
knot[i][j].NocallStartLen[p],
knot[i][j].NocallStartLen[p+1])
}
fmt.Printf("}")
}
}
}
fmt.Printf("\n")
}
}
return
} else if action == "sglfbarf" {
//_sglf,e := LoadGenomeLibraryCSV(c.String("sglf"))
_sglf, e := cglf.LoadGenomeLibraryCSV(c.String("sglf"))
if e != nil {
log.Fatal(e)
}
for path := range _sglf.LibInfo {
for step := range _sglf.LibInfo[path] {
for i := 0; i < len(_sglf.LibInfo[path][step]); i++ {
fmt.Printf("%x,%x,%x.%x.%x+%x\n", path, step,
_sglf.LibInfo[path][step][i].Path,
_sglf.LibInfo[path][step][i].Step,
_sglf.LibInfo[path][step][i].Variant,
_sglf.LibInfo[path][step][i].Span)
}
}
}
return
} else if action == "append" {
_sglf, e := cglf.LoadGenomeLibraryCSV(c.String("sglf"))
if e != nil {
log.Fatal(e)
}
ain_slice := make([]autoio.AutoioHandle, 0, 8)
for i := 0; i < len(inp_slice); i++ {
inp_fn := inp_slice[i]
ain, err := autoio.OpenReadScanner(inp_fn)
_ = ain
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer ain.Close()
ain_slice = append(ain_slice, ain)
break
}
path_str := c.String("path")
path_u64, e := strconv.ParseInt(path_str, 16, 64)
if e != nil {
log.Fatal(e)
}
path := int(path_u64)
cgf_bytes, e := ioutil.ReadFile(c.String("cgf"))
if e != nil {
log.Fatal(e)
}
//hdri,_ := headerintermediate_from_bytes(cgf_bytes[:])
hdri, _ := cgf.HeaderIntermediateFromBytes(cgf_bytes[:])
ctx := cgf.CGFContext{}
_cgf := cgf.CGF{}
_cgf.PathBytes = make([][]byte, 0, 1024)
cgf.CGFFillHeader(&_cgf, cgf_bytes)
ctx.CGF = &_cgf
ctx.SGLF = &_sglf
//CGFContext_construct_tilemap_lookup(&ctx)
ctx.ConstructTileMapLookup()
//allele_path,e := load_sample_fastj(&ain_slice[0])
allele_path, e := cgf.LoadSampleFastj(&ain_slice[0])
if e != nil {
log.Fatal(e)
}
//PathBytes,e := emit_path_bytes(&ctx, path, allele_path)
PathBytes, e := ctx.EmitPathBytes(path, allele_path)
if e != nil {
log.Fatal(e)
}
//headerintermediate_add_path(&hdri, path, PathBytes)
//write_cgf_from_intermediate(c.String("output"), &hdri)
cgf.HeaderIntermediateAddPath(&hdri, path, PathBytes)
cgf.WriteCGFFromIntermediate(c.String("output"), &hdri)
return
}
ain_slice := make([]autoio.AutoioHandle, 0, 8)
for i := 0; i < len(inp_slice); i++ {
inp_fn := inp_slice[i]
ain, err := autoio.OpenReadScanner(inp_fn)
_ = ain
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer ain.Close()
ain_slice = append(ain_slice, ain)
}
aout, err := autoio.CreateWriter(c.String("output"))
_ = aout
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer func() { aout.Flush(); aout.Close() }()
if c.Bool("pprof") {
gProfileFlag = true
gProfileFile = c.String("pprof-file")
}
if c.Bool("mprof") {
gMemProfileFlag = true
gMemProfileFile = c.String("mprof-file")
}
gVerboseFlag = c.Bool("Verbose")
if c.Int("max-procs") > 0 {
runtime.GOMAXPROCS(c.Int("max-procs"))
}
if gProfileFlag {
prof_f, err := os.Create(gProfileFile)
if err != nil {
fmt.Fprintf(os.Stderr, "Could not open profile file %s: %v\n", gProfileFile, err)
os.Exit(2)
}
pprof.StartCPUProfile(prof_f)
defer pprof.StopCPUProfile()
}
_sglf, e := cglf.LoadGenomeLibraryCSV(c.String("sglf"))
if e != nil {
log.Fatal(e)
}
ctx := cgf.CGFContext{}
_cgf := cgf.CGF{}
//header_bytes := cgf_default_header_bytes()
header_bytes := cgf.CGFDefaultHeaderBytes()
cgf.CGFFillHeader(&_cgf, header_bytes)
ctx.CGF = &_cgf
ctx.SGLF = &_sglf
//CGFContext_construct_tilemap_lookup(&ctx)
ctx.ConstructTileMapLookup()
for i := 0; i < len(ain_slice); i++ {
ain := ain_slice[i]
//allele_path,e := load_sample_fastj(&ain)
allele_path, e := cgf.LoadSampleFastj(&ain)
if e != nil {
log.Fatal(e)
}
p := 0x2c5
if i > 0 {
p = 0x247
}
//e = update_vector_path_simple(&ctx, p, allele_path)
e = ctx.UpdateVectorPathSimple(p, allele_path)
if len(ctx.CGF.StepPerPath) < len(ain_slice) {
ctx.CGF.StepPerPath = append(ctx.CGF.StepPerPath, uint64(len(_sglf.Lib[p])))
}
}
ctx.CGF.PathCount = uint64(len(_cgf.Path))
ctx.CGF.StepPerPath = make([]uint64, ctx.CGF.PathCount)
for i := uint64(0); i < ctx.CGF.PathCount; i++ {
ctx.CGF.StepPerPath[i] = uint64(len(_sglf.Lib[int(i)]))
}
//write_cgf(&ctx, "out.cgf")
ctx.WriteCGF("out.cgf")
}