func (g *FastJInfo) EmitAlignedInterleave(ref, alt0, alt1 []byte, out *bufio.Writer) {
length_bound := 10000
if len(ref) == 0 {
return
}
p0 := make([]byte, 0, len(ref))
p1 := make([]byte, 0, len(ref))
// We can bypass doing a string alignment if they're equal, so test
// for equal (considering 'n' (nocall) entries as wildcards).
//
if !_noc_eq(ref, alt0) {
if (len(ref) > length_bound) || (len(alt0) > length_bound) {
ref0, algn0 := g.ClumsyAlign(ref, alt0)
for ii := 0; ii < len(ref0); ii++ {
p0 = append(p0, pasta.SubMap[ref0[ii]][algn0[ii]])
}
} else {
ref0, algn0, sc0 := memz.Hirschberg(ref, alt0)
_ = sc0
for ii := 0; ii < len(ref0); ii++ {
p0 = append(p0, pasta.SubMap[ref0[ii]][algn0[ii]])
}
}
} else {
for ii := 0; ii < len(ref); ii++ {
p0 = append(p0, pasta.SubMap[ref[ii]][alt0[ii]])
}
}
if !_noc_eq(ref, alt1) {
if (len(ref) > length_bound) || (len(alt1) > length_bound) {
ref1, algn1 := g.ClumsyAlign(ref, alt1)
for ii := 0; ii < len(ref1); ii++ {
p1 = append(p1, pasta.SubMap[ref1[ii]][algn1[ii]])
}
} else {
ref1, algn1, sc1 := memz.Hirschberg(ref, alt1)
_ = sc1
for ii := 0; ii < len(ref1); ii++ {
p1 = append(p1, pasta.SubMap[ref1[ii]][algn1[ii]])
}
}
} else {
for ii := 0; ii < len(ref); ii++ {
p1 = append(p1, pasta.SubMap[ref[ii]][alt1[ii]])
}
}
r0 := bytes.NewReader(p0)
r1 := bytes.NewReader(p1)
g.Out = out
pasta.InterleaveStreams(r0, r1, g)
}
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)
}
}