-package main
+package lightning
import (
"bufio"
"net/http"
_ "net/http/pprof"
"os"
+ "strings"
"git.arvados.org/arvados.git/sdk/go/arvados"
log "github.com/sirupsen/logrus"
flags.IntVar(&f.MaxTag, "max-tag", -1, "drop tiles with tag ID > `N`")
}
+func (f *filter) Args() []string {
+ return []string{
+ fmt.Sprintf("-max-variants=%d", f.MaxVariants),
+ fmt.Sprintf("-min-coverage=%f", f.MinCoverage),
+ fmt.Sprintf("-max-tag=%d", f.MaxTag),
+ }
+}
+
func (f *filter) Apply(tilelib *tileLibrary) {
// Zero out variants at tile positions that have more than
// f.MaxVariants tile variants.
defer infile.Close()
}
log.Print("reading")
- cgs, err := ReadCompactGenomes(infile)
+ cgs, err := ReadCompactGenomes(infile, strings.HasSuffix(*inputFilename, ".gz"))
if err != nil {
return 1
}