func _main_fasta_to_pasta(c *cli.Context) {
var e error
infn_slice := c.StringSlice("input")
if len(infn_slice) < 1 {
infn_slice = append(infn_slice, "-")
}
ain, err := autoio.OpenReadScanner(infn_slice[0])
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Stderr.Sync()
os.Exit(1)
}
defer ain.Close()
fp := os.Stdin
if c.String("refstream") != "-" {
fp, e = os.Open(c.String("refstream"))
if e != nil {
fmt.Fprintf(os.Stderr, "%v", e)
os.Stderr.Sync()
os.Exit(1)
}
defer fp.Close()
}
ref_stream := bufio.NewReader(fp)
out := bufio.NewWriter(os.Stdout)
fi := FASTAInfo{}
fi.Init()
fi.Allele = 0
line_no := 0
fi.PastaBegin(out)
for ain.ReadScan() {
fasta_line := ain.ReadText()
line_no++
if len(fasta_line) == 0 || fasta_line == "" {
continue
}
e := fi.Pasta(fasta_line, ref_stream, out)
if e != nil {
fmt.Fprintf(os.Stderr, "ERROR: %v at line %v\n", e, line_no)
return
}
}
fi.PastaEnd(out)
}
func _main_gvcf_to_rotini(c *cli.Context) {
var e error
infn_slice := c.StringSlice("input")
if len(infn_slice) < 1 {
infn_slice = append(infn_slice, "-")
}
ain, err := autoio.OpenReadScanner(infn_slice[0])
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Stderr.Sync()
os.Exit(1)
}
defer ain.Close()
fp := os.Stdin
if c.String("refstream") != "-" {
fp, e = os.Open(c.String("refstream"))
if e != nil {
fmt.Fprintf(os.Stderr, "%v", e)
os.Stderr.Sync()
os.Exit(1)
}
defer fp.Close()
}
ref_stream := bufio.NewReader(fp)
out := bufio.NewWriter(os.Stdout)
g := gvcf.GVCFRefVar{}
g.Init()
line_no := 0
g.PastaBegin(out)
for ain.ReadScan() {
gvcf_line := ain.ReadText()
line_no++
if len(gvcf_line) == 0 || gvcf_line == "" {
continue
}
e := g.Pasta(gvcf_line, ref_stream, out)
if e != nil {
fmt.Fprintf(os.Stderr, "ERROR: %v at line %v\n", e, line_no)
return
}
}
g.PastaEnd(out)
out.Flush()
}
func _main_diff_to_rotini(c *cli.Context) {
infn_slice := c.StringSlice("input")
if len(infn_slice) < 1 {
infn_slice = append(infn_slice, "-")
}
ain, err := autoio.OpenReadScanner(infn_slice[0])
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Stderr.Sync()
os.Exit(1)
}
defer ain.Close()
diff_to_interleave(&ain)
}
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 load_Assembly(ctx *LanternContext, tagset_pdh, assembly_pdh string) error {
assembly_fn := ctx.Config.O["tagset"].O[tagset_pdh].O["assembly"].O[assembly_pdh].O["gz"].S
fp, e := autoio.OpenReadScanner(assembly_fn)
if e != nil {
return e
}
defer fp.Close()
log.Printf(">>>> loading assembly: %s\n", assembly_pdh)
if ctx.Assembly == nil {
ctx.Assembly = make(map[string]map[int][]int)
}
ctx.Assembly[assembly_pdh] = make(map[int][]int)
if ctx.AssemblyChrom == nil {
ctx.AssemblyChrom = make(map[string]map[int]string)
}
ctx.AssemblyChrom[assembly_pdh] = make(map[int]string)
path := 0
for fp.ReadScan() {
l := fp.ReadText()
if len(l) == 0 {
continue
}
if l[0] == '\n' {
continue
}
if l[0] == '>' {
parts := strings.Split(l[1:], ":")
name := parts[0]
_ = name
chrom := parts[1]
_ = chrom
path_s := parts[2]
_path, e := strconv.ParseInt(path_s, 16, 64)
if e != nil {
return e
}
path = int(_path)
ctx.Assembly[assembly_pdh][path] = make([]int, 0, 1024)
ctx.AssemblyChrom[assembly_pdh][path] = chrom
continue
}
_step, e := strconv.ParseInt(l[0:4], 16, 64)
if e != nil {
return e
}
step := int(_step)
_ = step
z := _skip_space(l[5:])
_ref_pos, e := strconv.ParseInt(z, 10, 64)
if e != nil {
return e
}
ref_pos := int(_ref_pos)
ctx.Assembly[assembly_pdh][path] = append(ctx.Assembly[assembly_pdh][path], ref_pos)
}
return nil
}
func (sglf *SGLF) AddGenomeLibraryCSV(fn string) error {
if sglf.Lib == nil {
sglf.Lib = make(map[int]map[int][]string)
}
if sglf.LibInfo == nil {
sglf.LibInfo = make(map[int]map[int][]SGLFInfo)
}
ain, e := autoio.OpenReadScanner(fn)
//if e!=nil { return sglf, e }
if e != nil {
return e
}
defer ain.Close()
line_no := -1
if sglf.MD5Lookup == nil {
sglf.MD5Lookup = make(map[string]SGLFInfo)
}
if sglf.PfxTagLookup == nil {
sglf.PfxTagLookup = make(map[string]SGLFInfo)
}
if sglf.SfxTagLookup == nil {
sglf.SfxTagLookup = make(map[string]SGLFInfo)
}
prev_pfxtag := ""
prev_sfxtag := ""
prev_sglf_info := SGLFInfo{}
prev_tilepath := -1
// There's a corner case when we're at the last tile and
// we add the sfx tag to SfxTagLookup. If one's already
// added, we can consult the 'can_overwrite' and notice that
// we shouldn't overwrite it. If we've added the sfxtag
// to the SfxTagLookup but then later notice it's the last
// tile, we can set the 'can_overwrite' entry to false
// to allow the addition of a future sfxtag.
//
// Tags are unique so it might never come up but if
// some variation at the end induces a run to be like a tag
// we could run into problems (though we might have other
// problems as well)
//
can_overwrite := make(map[string]bool)
for ain.ReadScan() {
line_no++
l := ain.ReadText()
if len(l) == 0 {
continue
}
if (l[0] == 0) || (l[0] == '#') {
continue
}
line_parts := strings.Split(l, ",")
//if len(line_parts)<3 { return sglf, fmt.Errorf("not enough CSV elements on line_no %d", line_no) }
if len(line_parts) < 3 {
return fmt.Errorf("not enough CSV elements on line_no %d", line_no)
}
tileid_span_parts := strings.Split(line_parts[0], "+")
//if len(tileid_span_parts)!=2 { return sglf, fmt.Errorf("invalid tileid (%s) on line_no %d", line_parts[0], line_no) }
if len(tileid_span_parts) != 2 {
return fmt.Errorf("invalid tileid (%s) on line_no %d", line_parts[0], line_no)
}
tileid_parts := strings.Split(tileid_span_parts[0], ".")
//if len(tileid_parts)!=4 { return sglf, fmt.Errorf("invalid tileid (%s) on line_no %d", line_parts[0], line_no) }
if len(tileid_parts) != 4 {
return fmt.Errorf("invalid tileid (%s) on line_no %d", line_parts[0], line_no)
}
tilepath_l, e := strconv.ParseInt(tileid_parts[0], 16, 64)
//if e!=nil { return sglf, fmt.Errorf("%v: line_no %d\n", e, line_no) }
if e != nil {
return fmt.Errorf("%v: line_no %d\n", e, line_no)
}
tilestep_l, e := strconv.ParseInt(tileid_parts[2], 16, 64)
//if e!=nil { return sglf, fmt.Errorf("%v: line_no %d\n", e, line_no) }
if e != nil {
return fmt.Errorf("%v: line_no %d\n", e, line_no)
}
tilevar_l, e := strconv.ParseInt(tileid_parts[3], 16, 64)
//if e!=nil { return sglf, fmt.Errorf("%v: line_no %d\n", e, line_no) }
if e != nil {
return fmt.Errorf("%v: line_no %d\n", e, line_no)
}
//tilespan_l,e := strconv.ParseInt(tileid_span_parts[1], 16, 64)
tilespan_l, e := strconv.ParseInt(tileid_span_parts[1], 10, 64)
//if e!=nil { return sglf, fmt.Errorf("%v: line_no %d\n", e, line_no) }
if e != nil {
return fmt.Errorf("%v: line_no %d\n", e, line_no)
}
tilepath := int(tilepath_l)
tilestep := int(tilestep_l)
tilevar := int(tilevar_l)
tilespan := int(tilespan_l)
md5_str := line_parts[1]
seq := line_parts[2]
//if len(seq) < 48 { return sglf, fmt.Errorf("len(seq)<48: line_no %d", line_no) }
if len(seq) < 48 {
return fmt.Errorf("len(seq)<48: line_no %d", line_no)
}
pfxtag := seq[:24]
sfxtag := seq[len(seq)-24:]
if _, ok := sglf.Lib[tilepath]; !ok {
sglf.Lib[tilepath] = make(map[int][]string)
sglf.LibInfo[tilepath] = make(map[int][]SGLFInfo)
}
if _, ok := sglf.Lib[tilepath][tilestep]; !ok {
sglf.Lib[tilepath][tilestep] = make([]string, 0, 16)
sglf.LibInfo[tilepath][tilestep] = make([]SGLFInfo, 0, 16)
}
sglf.Lib[tilepath][tilestep] = append(sglf.Lib[tilepath][tilestep], seq)
sglf.LibInfo[tilepath][tilestep] = append(sglf.LibInfo[tilepath][tilestep], SGLFInfo{Path: tilepath, Step: tilestep, Variant: tilevar, Span: tilespan})
sglf_info := SGLFInfo{Path: int(tilepath), Step: int(tilestep), Variant: int(tilevar), Span: int(tilespan)}
sglf.MD5Lookup[md5_str] = sglf_info
if prev_pfxtag != "" {
sglf.PfxTagLookup[prev_pfxtag] = prev_sglf_info
}
if prev_sfxtag != "" {
if _, ok := can_overwrite[prev_sfxtag]; !ok {
//DEBUG
//fmt.Printf(">>> adding prev_sfxtag %s\n", prev_sfxtag)
// not in map, add it
//
sglf.SfxTagLookup[prev_sfxtag] = prev_sglf_info
} else if can_overwrite[prev_sfxtag] {
log.Printf("found suspicious tag (previously seen): '%s' at path.step.variant (%x.%x.%x)",
prev_sfxtag, tilepath, tilestep, tilevar)
// otherwise if we can overwrite it, do so
//
sglf.SfxTagLookup[prev_sfxtag] = prev_sglf_info
}
// Remember we've added this sfxtag
//
can_overwrite[prev_sfxtag] = false
}
if prev_tilepath != tilepath {
if tilestep > 0 {
can_overwrite[prev_sfxtag] = true
}
prev_pfxtag = ""
prev_sfxtag = ""
//fmt.Printf("######\n")
}
prev_sfxtag = sfxtag
if tilestep > 0 {
prev_pfxtag = pfxtag
}
prev_sglf_info = sglf_info
prev_tilepath = tilepath
//fmt.Printf("%d: %x.%x %s (%s) %s (%s)\n", line_no, tilepath, tilestep, prev_pfxtag, pfxtag, prev_sfxtag, sfxtag)
//fmt.Printf(":%s:\n", l)
//os.Exit(0)
}
if prev_pfxtag != "" {
sglf.PfxTagLookup[prev_pfxtag] = prev_sglf_info
}
//return sglf, nil
return nil
}
func _main_gff_to_rotini(c *cli.Context) {
var e error
infn_slice := c.StringSlice("input")
if len(infn_slice) < 1 {
infn_slice = append(infn_slice, "-")
}
ain, err := autoio.OpenReadScanner(infn_slice[0])
if err != nil {
fmt.Fprintf(os.Stderr, "%v", err)
os.Stderr.Sync()
os.Exit(1)
}
defer ain.Close()
fp := os.Stdin
if c.String("refstream") != "-" {
fp, e = os.Open(c.String("refstream"))
if e != nil {
fmt.Fprintf(os.Stderr, "%v", e)
os.Stderr.Sync()
os.Exit(1)
}
defer fp.Close()
}
ref_stream := bufio.NewReader(fp)
out := bufio.NewWriter(os.Stdout)
gff := GFFRefVar{}
gff.Init()
if len(c.String("chrom")) > 0 {
gff.Chrom(c.String("chrom"))
}
if c.Int("start") > 0 {
gff.RefPos = c.Int("start")
gff.PrevRefPos = gff.RefPos
}
line_no := 0
gff.PastaBegin(out)
for ain.ReadScan() {
gff_line := ain.ReadText()
line_no++
if len(gff_line) == 0 || gff_line == "" {
continue
}
e := gff.Pasta(gff_line, ref_stream, out)
//if e == io.EOF { break }
if (e != io.EOF) && (e != nil) {
fmt.Fprintf(os.Stderr, "ERROR: %v at line %v\n", e, line_no)
return
}
}
e = gff.PastaRefEnd(ref_stream, out)
if (e != io.EOF) && (e != nil) {
fmt.Fprintf(os.Stderr, "ERROR: GFF PastaRefEnd: %v at line %v\n", e, line_no)
return
}
gff.PastaEnd(out)
}
