func _main(c *cli.Context) {
g_START_SEQUENCEID = c.Int("start-sequence-id")
g_START_GRAPHJOINID = c.Int("start-graphjoin-id")
g_FASTAID = c.Int("fasta-id")
g_VARIANTSETID = c.Int("variantset-id")
if c.Bool("pprof") {
gProfileFlag = true
gProfileFile = c.String("pprof-file")
}
if c.Bool("mprof") {
gMemProfileFlag = true
gMemProfileFile = c.String("mprof-file")
}
g_show_progress = c.Bool("progress")
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()
}
fasta_ofn := c.String("fasta")
sequence_ofn := c.String("sequence")
graphjoin_ofn := c.String("graphjoin")
fasta_csv_ofn := c.String("fasta-csv")
graphjoin_variantset_ofn := c.String("graphjoin-variantset")
fasta_out, err := autoio.CreateWriter(fasta_ofn)
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer func() { fasta_out.Flush(); fasta_out.Close() }()
fasta_csv_out, err := autoio.CreateWriter(fasta_csv_ofn)
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer func() { fasta_csv_out.Flush(); fasta_csv_out.Close() }()
seq_out, err := autoio.CreateWriter(sequence_ofn)
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer func() { seq_out.Flush(); seq_out.Close() }()
gj_out, err := autoio.CreateWriter(graphjoin_ofn)
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer func() { gj_out.Flush(); gj_out.Close() }()
vs_gj_out, err := autoio.CreateWriter(graphjoin_variantset_ofn)
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer func() { vs_gj_out.Flush(); vs_gj_out.Close() }()
// Process input FastJ files
ifns := c.StringSlice("input")
for i := 0; i < len(ifns); i++ {
if g_show_progress {
fmt.Fprintf(os.Stderr, ">>> %s\n", ifns[i])
}
name := ifns[i]
ifn := ifns[i]
if strings.Contains(ifns[i], ",") {
z := strings.SplitN(ifns[i], ",", 2)
name = z[0]
ifn = z[1]
}
e := import_fastj(name, ifn)
if e != nil {
log.Fatal(e)
}
}
// Once the library has been created, rank
// the resulting tiles.
//
rank_tile_lib()
// Output a big FASTA file with all of our
// sequence information.
//
emit_fasta(fasta_out.Writer)
// And our FASTA.csv file
//
emit_fasta_sql_csv(fasta_csv_out.Writer, fasta_ofn)
// Now output the SQL Sequences.
//
emit_sequences(seq_out.Writer)
// Now emit the SQL GraphJoin
//
emit_graphjoin(gj_out.Writer)
emit_graphjoin_variantset(vs_gj_out.Writer)
}
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")
}
func _main(c *cli.Context) {
sequence_ifn := c.String("sequence")
if len(sequence_ifn) == 0 {
cli.ShowAppHelp(c)
}
g_ALLELE_ID = c.Int("start-allele-id")
g_START_CALLSET_ID = c.Int("start-callset-id")
g_START_VARIANTSET_ID = c.Int("start-variantset-id")
g_VARIANTSET_NAME = c.String("variantset-name")
ifns := c.StringSlice("input")
if len(ifns) == 0 {
cli.ShowAppHelp(c)
}
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()
}
allele_ofn := c.String("allele")
allele_path_item_ofn := c.String("allele-path")
callset_ofn := c.String("callset")
allele_call_ofn := c.String("allele-call")
variantset_ofn := c.String("variantset")
variantset_callset_ofn := c.String("variantset-callset-join")
allele_out, err := autoio.CreateWriter(allele_ofn)
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer func() { allele_out.Flush(); allele_out.Close() }()
allele_path_item_out, err := autoio.CreateWriter(allele_path_item_ofn)
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer func() { allele_path_item_out.Flush(); allele_path_item_out.Close() }()
callset_out, err := autoio.CreateWriter(callset_ofn)
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer func() { callset_out.Flush(); callset_out.Close() }()
allele_call_out, err := autoio.CreateWriter(allele_call_ofn)
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer func() { allele_call_out.Flush(); allele_call_out.Close() }()
variantset_out, err := autoio.CreateWriter(variantset_ofn)
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer func() { variantset_out.Flush(); variantset_out.Close() }()
variantset_callset_out, err := autoio.CreateWriter(variantset_callset_ofn)
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer func() { variantset_callset_out.Flush(); variantset_callset_out.Close() }()
show_progress_flag := c.Bool("progress")
// We only use one variant set
//
add_variantset(g_START_VARIANTSET_ID, g_VARIANTSET_NAME)
// Process Sequence CSV file
//
import_sequence(sequence_ifn)
// First populate the callset maps
//
for i := 0; i < len(ifns); i++ {
name := ifns[i]
if strings.Contains(ifns[i], ",") {
z := strings.SplitN(ifns[i], ",", 2)
name = z[0]
}
g_callset[name] = CallSet{g_START_CALLSET_ID + i, name, name}
}
// Process input FastJ files
//
for i := 0; i < len(ifns); i++ {
name := ifns[i]
ifn := ifns[i]
if strings.Contains(ifns[i], ",") {
z := strings.SplitN(ifns[i], ",", 2)
name = z[0]
ifn = z[1]
}
if show_progress_flag {
fmt.Printf(">>>> %s %s\n", name, ifn)
}
e := import_fastj(name, ifn)
if e != nil {
log.Fatal(e)
}
}
// Variant Sets
//
emit_variantset(variantset_out.Writer)
// Output the CallSet
//
emit_callset(callset_out.Writer)
emit_variantset_callset_join(variantset_callset_out.Writer)
// Output Allele information
//
emit_allele(allele_out.Writer)
//
emit_allele_call(allele_call_out.Writer)
// Output actual path
//
emit_allele_path_item(allele_path_item_out.Writer)
}
func _main(c *cli.Context) {
gLanternStat = LanternStatStruct{}
gLanternStat.StartTime = time.Now()
ctx := &LanternContext{}
//DEBUG
ctx.VerboseFlag = true
ctx.PrettyAPIFlag = true
ctx.VerboseAPIFlag = true
e := _load_json_config(ctx, c.String("config"))
if e != nil {
log.Fatal(e)
}
tagset_pdh := "dad7041d432965cd07a4ad8e0aad1b6e"
assembly_pdh := "aa39590be6f1812f0a792dd4c86678e8+1348"
if ctx.VerboseFlag {
log.Printf("loading assembly %v (tagset %v)\n", assembly_pdh, tagset_pdh)
}
e = load_Assembly(ctx, tagset_pdh, assembly_pdh)
if e != nil {
log.Fatal(e)
}
if ctx.VerboseFlag {
log.Printf("assembly loaded\n")
}
//e = ctx.LoadCGFBytes(ctx.Config.O["cgf"].O["dir"].S)
e = ctx.LoadCGFBytesConfig()
if e != nil {
log.Fatal(e)
}
if ctx.VerboseFlag {
log.Printf("cgf bytes loaded\n")
}
ctx.LoadCGFIntermediate()
for sglf_name, _ := range ctx.Config.O["tagset"].O[tagset_pdh].O["sglf"].O {
_path, e := strconv.ParseInt(sglf_name, 16, 64)
if e != nil {
log.Fatal(e)
}
ipath := int(_path)
ctx.LoadSGLF(ipath, ctx.Config.O["tagset"].O[tagset_pdh].O["sglf"].O[sglf_name].S)
}
log.Printf("PreCalc starting...\n")
ctx.PreCalc()
log.Printf("PreCalc done\n")
/*
//DEBUG
fmt.Printf("testing...\n")
for pdh := range ctx.Assembly {
for path := range ctx.Assembly[pdh] {
for i:=0; i<len(ctx.Assembly[pdh][path]); i++ {
fmt.Printf("%v %v %v\n", pdh, path, ctx.Assembly[pdh][path][i])
}
}
os.Exit(0)
}
for pdh := range ctx.AssemblyChrom {
for path := range ctx.AssemblyChrom[pdh] {
fmt.Printf("%v %v %v\n", pdh, path, ctx.AssemblyChrom[pdh][path])
}
}
fmt.Printf("cp\n")
*/
/*
if c.String("input") == "" {
fmt.Fprintf( os.Stderr, "Input required, exiting\n" )
cli.ShowAppHelp( c )
os.Exit(1)
}
ain,err := autoio.OpenScanner( c.String("input") ) ; _ = ain
if err!=nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Exit(1)
}
defer ain.Close()
*/
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 )
var err error
g_pprof, 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()
pprof.StartCPUProfile(g_pprof)
}
// Start server
//
//listener,err := net.Listen("tcp", gPortStr)
//if err!=nil { log.Fatal(err) }
term := make(chan os.Signal, 1)
go func(sig <-chan os.Signal) {
s := <-sig
if gVerboseFlag {
fmt.Printf("caught signal: %v\n", s)
//listener.Close()
}
}(term)
signal.Notify(term, syscall.SIGTERM)
signal.Notify(term, syscall.SIGHUP)
// Set up routing
//
router := httprouter.New()
router.POST("/", handle_json_req)
router.GET("/", index)
//router.GET("/status", handle_status)
router.GET("/status", ctx.APIStatus)
router.GET("/cgf-stats", ctx.CGFSimpleStats)
//router.GET("/qux", func(w http.ResponseWriter, r *http.Request, params httprouter.Params) { ctx.Qux(w,r, params); } )
router.GET("/qux", ctx.Qux)
router.GET("/assemblies", ctx.APIAssemblies)
router.GET("/assemblies/:id", ctx.APIAssembliesId)
//router.GET("/callsets", handle_callsets)
//router.GET("/tile-library/tag-sets", handle_tile_library_tag_sets)
//router.GET("/tile-library/tag-sets/:tagset_id", handle_tile_library_tag_sets_id)
//router.GET("/tile-library/tag-sets/:tagset_id/paths", handle_tile_library_tag_sets_id_paths)
//router.GET("/tile-library/tag-sets/:tagset_id/paths/:path_id", handle_tile_library_tag_sets_id_paths_id)
//router.GET("/tile-library/tag-sets/:tagset_id/tile-positions", handle_tile_library_tag_sets_id_tile_positions)
//router.GET("/tile-library/tag-sets/:tagset_id/tile-positions/:tilepos_id", handle_tile_library_tag_sets_id_tile_positions_id)
//router.GET("/tile-library/tag-sets/:tagset_id/tile-positions/:tilepos_id/locus", handle_tile_library_tag_sets_id_tile_positions_id_locus)
router.GET("/tile-library/tag-sets", ctx.APITileLibraryTagSets)
router.GET("/tile-library/tag-sets/:tagset_id", ctx.APITileLibraryTagSetsId)
router.GET("/tile-library/tag-sets/:tagset_id/paths", ctx.APITileLibraryTagSetsIdPaths)
router.GET("/tile-library/tag-sets/:tagset_id/paths/:path_id", ctx.APITileLibraryTagSetsIdPathsId)
router.GET("/tile-library/tag-sets/:tagset_id/tile-positions", ctx.APITileLibraryTagSetsIdTilePositions)
router.GET("/tile-library/tag-sets/:tagset_id/tile-positions/:tilepos_id", ctx.APITileLibraryTagSetsIdTilePositionsId)
router.GET("/tile-library/tag-sets/:tagset_id/tile-positions/:tilepos_id/locus", ctx.APITileLibraryTagSetsIdTilePositionsIdLocus)
router.GET("/tile-library/tag-sets/:tagset_id/tile-variants", ctx.APITileLibraryTagSetsIdTileVariants)
router.GET("/tile-library/tag-sets/:tagset_id/tile-variants/:tilevariant_id", ctx.APITileLibraryTagSetsIdTileVariantsId)
router.GET("/tile-library/tag-sets/:tagset_id/tile-variants/:tilevariant_id/locus", ctx.APITileLibraryTagSetsIdTileVariantsIdLocus)
router.GET("/callsets", ctx.APICallsets)
router.GET("/callsets/:callset_id", ctx.APICallsetsId)
router.GET("/callsets/:callset_id/tile-variants", ctx.APICallsetsIdTileVariants)
//router.GET("/tile-library/tag-sets/:tagset_id/tile-variants", handle_tile_library_tag_sets_id_tile_variants)
//router.GET("/tile-library/tag-sets/:tagset_id/tile-variants/:tilevariant_id", handle_tile_library_tag_sets_id_tile_variants_id)
//router.GET("/tile-library/tag-sets/:tagset_id/tile-variants/:tilevariant_id/locus", handle_tile_library_tag_sets_id_tile_variants_id_locus)
//router.GET("/tile-library/tag-sets/:tagset_id/tile-variants/:tilevariant_id/subsequence", handle_tile_library_tag_sets_id_tile_variants_id_subsequence)
//router.GET("/tile-library/tag-sets/:tagset_id/tile-variants/:tilevariant_id/annotations", handle_tile_library_tag_sets_id_tile_variants_id_annotations)
/*
http.HandleFunc("/", handle_json_req)
http.HandleFunc("/status", handle_status)
http.HandleFunc("/assemblies/", handle_assemblies_id)
http.HandleFunc("/assemblies", handle_assemblies)
*/
if gVerboseFlag {
fmt.Printf("listening: %v\n", gPortStr)
}
http.ListenAndServe(gPortStr, router)
//listener,err := net.Listen("tcp", gPortStr)
//if err!=nil { log.Fatal(err) }
//defer listener.Close()
//e := http.Serve(listener, router)
if gVerboseFlag {
fmt.Printf("shutting down\n")
}
}
func _main(c *cli.Context) {
var e error
action := "echo"
msg_slice := c.StringSlice("Message")
msg_str := ""
for i := 0; i < len(msg_slice); i++ {
msg_str += ">" + msg_slice[i]
}
//if c.String("action") != "" { action = c.String("action") }
if len(c.String("action")) == 0 {
cli.ShowAppHelp(c)
return
}
action = c.String("action")
if action == "diff-rotini" {
_main_diff_to_rotini(c)
return
} else if action == "gff-rotini" {
_main_gff_to_rotini(c)
return
} else if action == "gff-pasta" {
_main_gff_to_pasta(c)
return
} else if action == "gvcf-rotini" {
_main_gvcf_to_rotini(c)
return
} else if action == "cgivar-pasta" {
_main_cgivar_to_pasta(c)
return
} else if action == "cgivar-rotini" {
_main_cgivar_to_rotini(c)
return
} else if action == "fasta-pasta" {
_main_fasta_to_pasta(c)
return
}
infn_slice := c.StringSlice("input")
var stream *bufio.Reader
var stream_b *bufio.Reader
g_debug = c.Bool("debug")
gFullRefSeqFlag = c.Bool("full-sequence")
gFullNocSeqFlag = c.Bool("full-nocall-sequence")
n_inp_stream := 0
if len(infn_slice) > 0 {
fp := os.Stdin
if infn_slice[0] != "-" {
fp, e = os.Open(infn_slice[0])
if e != nil {
fmt.Fprintf(os.Stderr, "%v", e)
os.Stderr.Sync()
os.Exit(1)
}
defer fp.Close()
}
stream = bufio.NewReader(fp)
n_inp_stream++
}
if len(infn_slice) > 1 {
fp, e := os.Open(infn_slice[1])
if e != nil {
fmt.Fprintf(os.Stderr, "%v", e)
os.Stderr.Sync()
os.Exit(1)
}
defer fp.Close()
stream_b = bufio.NewReader(fp)
n_inp_stream++
action = "interleave"
}
aout, err := autoio.CreateWriter(c.String("output"))
_ = aout
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Stderr.Sync()
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.Stderr.Sync()
os.Exit(2)
}
pprof.StartCPUProfile(prof_f)
defer pprof.StopCPUProfile()
}
if (action != "ref-rstream") && (action != "rstream") && (n_inp_stream == 0) {
if action == "interleave" {
fmt.Fprintf(os.Stderr, "Provide input stream")
cli.ShowAppHelp(c)
os.Stderr.Sync()
os.Exit(1)
}
stream = bufio.NewReader(os.Stdin)
}
//---
if action == "echo" {
echo_stream(stream)
} else if action == "filter-pasta" {
out := bufio.NewWriter(os.Stdout)
pasta_filter(stream, out, c.Int("start"), c.Int("n"))
out.Flush()
} else if action == "filter-rotini" {
out := bufio.NewWriter(os.Stdout)
interleave_filter(stream, out, c.Int("start"), c.Int("n"))
out.Flush()
} else if action == "interleave" {
pasta.InterleaveStreams(stream, stream_b, os.Stdout)
} else if action == "ref-rstream" {
r_ctx := random_stream_context_from_param(c.String("param"))
random_ref_stream(r_ctx)
} else if action == "rstream" {
r_ctx := random_stream_context_from_param(c.String("param"))
random_stream(r_ctx)
//FASTA
} else if action == "pasta-fasta" {
fi := FASTAInfo{}
fi.Init()
out := bufio.NewWriter(os.Stdout)
fi.Header(out)
e := fi.Stream(stream, out)
if e != nil {
fmt.Fprintf(os.Stderr, "\nERROR: %v\n", e)
os.Stderr.Sync()
os.Exit(1)
}
fi.PrintEnd(out)
} else if action == "diff-rotini" {
//e:=diff_to_interleave(&stream)
//if e!=nil { fmt.Fprintf(os.Stderr, "%v\n", e); return }
} else if action == "rotini-diff" {
e := interleave_to_diff(stream, simple_refvar_printer)
if e != nil {
fmt.Fprintf(os.Stderr, "%v\n", e)
return
}
} else if action == "rotini" {
} else if action == "pasta-ref" {
e := pasta_to_haploid(stream, -1)
if e != nil {
fmt.Fprintf(os.Stderr, "\nERROR: %v\n", e)
os.Stderr.Sync()
os.Exit(1)
}
} else if action == "rotini-ref" {
e := interleave_to_haploid(stream, -1)
if e != nil {
fmt.Fprintf(os.Stderr, "\nERROR: %v\n", e)
os.Stderr.Sync()
os.Exit(1)
}
} else if action == "rotini-alt0" {
interleave_to_haploid(stream, 0)
} else if action == "rotini-alt1" {
interleave_to_haploid(stream, 1)
} else if action == "rotini-gff" {
gff := GFFRefVar{}
gff.Init()
e := interleave_to_diff_iface(stream, &gff, os.Stdout)
if e != nil {
fmt.Fprintf(os.Stderr, "%v\n", e)
return
}
} else if action == "rotini-gvcf" {
g := gvcf.GVCFRefVar{}
g.Init()
// We need the full reference sequence for beginning and ending bases
//
gFullRefSeqFlag = true
e := interleave_to_diff_iface(stream, &g, os.Stdout)
if e != nil {
fmt.Fprintf(os.Stderr, "%v\n", e)
return
}
} else if action == "rotini-cgivar" {
cgivar := CGIRefVar{}
cgivar.Init()
e := interleave_to_diff_iface(stream, &cgivar, os.Stdout)
if e != nil {
fmt.Fprintf(os.Stderr, "%v\n", e)
return
}
} else if action == "fastj-rotini" {
//
// FastJ to rotini
//
fp := os.Stdin
if c.String("refstream") != "-" {
fp, e = os.Open(c.String("refstream"))
if e != nil {
fmt.Fprintf(os.Stderr, "ERROR: opening reference stream: %v", e)
os.Stderr.Sync()
os.Exit(1)
}
defer fp.Close()
}
ref_stream := bufio.NewReader(fp)
assembly_fp, e := os.Open(c.String("assembly"))
if e != nil {
fmt.Fprintf(os.Stderr, "ERROR: opening assembly stream: %v", e)
os.Stderr.Sync()
os.Exit(1)
}
defer assembly_fp.Close()
assembly_stream := bufio.NewReader(assembly_fp)
out := bufio.NewWriter(os.Stdout)
fji := FastJInfo{}
fji.RefPos = c.Int("start")
fji.Chrom = c.String("chrom")
e = fji.Pasta(stream, ref_stream, assembly_stream, out)
if e != nil {
fmt.Fprintf(os.Stderr, "ERROR: processing PASTA stream: %v\n", e)
os.Stderr.Sync()
os.Exit(1)
}
} else if action == "rotini-fastj" {
//
// rotini to FastJ
//
tag_fp, e := os.Open(c.String("tag"))
if e != nil {
fmt.Fprintf(os.Stderr, "%v", e)
os.Stderr.Sync()
os.Exit(1)
}
defer tag_fp.Close()
assembly_fp, e := os.Open(c.String("assembly"))
if e != nil {
fmt.Fprintf(os.Stderr, "%v", e)
os.Stderr.Sync()
os.Exit(1)
}
defer assembly_fp.Close()
tag_reader := bufio.NewReader(tag_fp)
assembly_reader := bufio.NewReader(assembly_fp)
fji := FastJInfo{}
fji.RefPos = c.Int("start")
fji.RefBuild = c.String("build")
fji.Chrom = c.String("chrom")
_tilepath, e := strconv.ParseUint(c.String("tilepath"), 16, 64)
if e != nil {
fmt.Fprintf(os.Stderr, "%v", e)
os.Stderr.Sync()
os.Exit(1)
}
fji.TagPath = int(_tilepath)
out := bufio.NewWriter(os.Stdout)
err := fji.Convert(stream, tag_reader, assembly_reader, out)
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Stderr.Sync()
os.Exit(1)
}
} else {
fmt.Printf("invalid action (%s)\n", action)
os.Stderr.Sync()
os.Exit(1)
}
}