func main() {
var seq_file = flag.String("s", "", "Specify a file containing the sequence.")
var rl = flag.Int("l", 100, "Read length.")
var coverage = flag.Float64("c", 2.0, "Coverage")
var error_rate = flag.Float64("e", 0.01, "Error rate.")
flag.BoolVar(&Debug, "debug", false, "Turn on debug mode.")
flag.Parse()
read_len := int(*rl)
if *seq_file != "" {
if *coverage > 0 && read_len > 0 {
idx := fmi.New(*seq_file)
num_of_reads := int(*coverage * float64(idx.LEN) / float64(read_len))
read_indices := make([]int, num_of_reads)
the_read := make([]byte, read_len)
var rand_pos int
for i := 0; i < num_of_reads; i++ {
rand_pos = int(rand_gen.Intn(int(idx.LEN - read_len)))
if justN(rand_pos, int(read_len)) {
i--
continue
}
read_indices = idx.Repeat(rand_pos, read_len)
var errors []int
if int(rand_pos+read_len) >= len(fmi.SEQ) {
panic("Read may be shorter than wanted.")
}
copy(the_read, fmi.SEQ[rand_pos:rand_pos+read_len])
for k := 0; k < len(the_read); k++ {
if rand_gen.Float64() < *error_rate {
the_read[k] = random_error(the_read[k])
errors = append(errors, k)
}
}
if Debug {
for j := 0; j < int(rand_pos); j++ {
fmt.Printf(" ")
}
}
fmt.Printf("%s %d ", the_read, len(read_indices))
for j := 0; j < len(read_indices); j++ {
fmt.Printf("%d ", read_indices[j])
}
fmt.Printf("%d", len(errors))
for j := 0; j < len(errors); j++ {
fmt.Printf(" %d", errors[j])
}
fmt.Println()
}
} else {
idx := fmi.New(*seq_file)
idx.Save(*seq_file)
}
} else {
fmt.Println("Must provide sequence file")
}
}
//-----------------------------------------------------------------------------
func main() {
idx := fmi.New(os.Args[1])
memstats := new(runtime.MemStats)
runtime.ReadMemStats(memstats)
fmt.Printf("memstats before GC: bytes = %d footprint = %d\n", memstats.HeapAlloc, memstats.Sys)
fmt.Println("Size\t", len(idx.SA))
}
//-----------------------------------------------------------------------------
func main() {
var build_file = flag.String("build", "", "Specify a file, from which to build FM index.")
var index_file = flag.String("i", "", "index file")
var queries_file = flag.String("q", "", "queries file")
flag.BoolVar(&Debug, "debug", false, "Turn on debug mode.")
flag.Parse()
if *build_file != "" {
idx := fmi.New(*build_file)
idx.Save(*build_file)
} else if *index_file != "" && *queries_file != "" {
idx := fmi.Load(*index_file)
f, err := os.Open(*queries_file)
if err != nil {
panic("error opening file " + *queries_file)
}
r := bufio.NewReader(f)
for {
line, err := r.ReadBytes('\n')
if err != nil {
break
}
if len(line) > 1 {
line = line[0 : len(line)-1]
result := idx.Search(line)
if len(result) == 0 {
fmt.Println("na")
} else {
for _, v := range result {
fmt.Printf("%d ", v)
}
fmt.Println()
}
}
}
}
}