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main.go
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main.go
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package main
import (
"bufio"
"fmt"
"io"
"log"
"os"
"strconv"
_ "github.com/mattn/go-sqlite3"
"github.com/jmoiron/sqlx"
"github.com/mnsmar/htsdb"
"gopkg.in/alecthomas/kingpin.v2"
)
const prog = "htsdb-to-sam"
const version = "0.1"
const descr = `Print database records in SAM format. Provided SQL filters will
apply to output.`
var (
app = kingpin.New(prog, descr)
dbFile = app.Flag("db", "SQLite file.").
PlaceHolder("<file>").Required().String()
tab = app.Flag("table", "Database table name.").
Default("sample").String()
where = app.Flag("where", "SQL filter injected in WHERE clause.").
PlaceHolder("<SQL>").String()
header = app.Flag("header", "build and print SAM header.").
Bool()
verbose = app.Flag("verbose", "Verbose mode.").Short('v').Bool()
)
// Reader encapsulates a connection to a database and implements io.Reader.
type Reader struct {
db *sqlx.DB
dest *htsdb.SamRecord
rows *sqlx.Rows
err error
}
// NewReader returns a new Reader that reads from db using the given query.
func NewReader(db *sqlx.DB, query string) (*Reader, error) {
rows, err := db.Queryx(query)
if err != nil {
return nil, err
}
return &Reader{
db: db,
dest: &htsdb.SamRecord{},
rows: rows,
}, nil
}
// Read reads the next record from r into p. It returns the number of bytes
// read (0 <= n <= len(p)) and any error encountered. Even if Read returns n <
// len(p), it may use all of p as scratch space during the call. If some data
// is available but not len(p) bytes, Read conventionally returns what is
// available instead of waiting for more. It will return n = 0 and io.EOF when
// r is exhausted. It will return n = 0 and an error if it encounters one.
func (r *Reader) Read(p []byte) (n int, err error) {
if len(p) == 0 {
return 0, nil
}
ok := r.rows.Next()
if !ok {
if r.rows.Err() == nil {
return 0, io.EOF
}
return 0, r.rows.Err()
}
err = r.rows.StructScan(r.dest)
if err != nil {
return 0, err
}
s := r.dest.Qname + "\t" +
strconv.Itoa(r.dest.Flag) + "\t" +
r.dest.Rname + "\t" +
strconv.Itoa(r.dest.Pos) + "\t" +
strconv.Itoa(r.dest.Mapq) + "\t" +
r.dest.Cigar + "\t" +
r.dest.Rnext + "\t" +
strconv.Itoa(r.dest.Pnext) + "\t" +
strconv.Itoa(r.dest.Tlen) + "\t" +
r.dest.Seq + "\t" +
r.dest.Qual + "\t" +
r.dest.Tags + "\n"
n = copy(p, s[0:])
return
}
func main() {
app.HelpFlag.Short('h')
app.Version(version)
_, err := app.Parse(os.Args[1:])
if err != nil {
kingpin.Fatalf("%s", err)
}
db, err := sqlx.Connect("sqlite3", *dbFile)
if err != nil {
log.Fatal(err)
}
readsB := htsdb.SamRecordBuilder.From(*tab)
refsB := htsdb.ReferenceBuilder.From(*tab)
if *where != "" {
readsB = readsB.Where(*where)
refsB = refsB.Where(*where)
}
query, _, err := readsB.ToSql()
if err != nil {
log.Fatal(err)
}
if *header == true {
refs, err := htsdb.SelectReferences(db, refsB)
if err != nil {
log.Fatal(err)
}
for _, r := range refs {
fmt.Printf("@SQ\tSN:%s\tLN:%d\n", r.Name(), r.Len())
}
}
r, err := NewReader(db, query)
if err != nil {
log.Fatal(err)
}
sc := bufio.NewScanner(r)
for {
ok := sc.Scan()
if ok == false {
break
}
fmt.Printf("%s\n", sc.Text())
}
if sc.Err() != nil {
log.Fatal(err)
}
}