X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/2828ecdafbfe8838efcfaa0c6b3c456a2bf7d745..HEAD:/filter.go

diff --git a/filter.go b/filter.go
deleted file mode 100644
index 89aa778f8b..0000000000
--- a/filter.go
+++ /dev/null
@@ -1,194 +0,0 @@
-package main
-
-import (
-	"bufio"
-	"encoding/gob"
-	"errors"
-	"flag"
-	"fmt"
-	"io"
-	"io/ioutil"
-	"net/http"
-	_ "net/http/pprof"
-	"os"
-
-	"git.arvados.org/arvados.git/sdk/go/arvados"
-	log "github.com/sirupsen/logrus"
-)
-
-type filterer struct {
-	output io.Writer
-}
-
-func (cmd *filterer) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
-	var err error
-	defer func() {
-		if err != nil {
-			fmt.Fprintf(stderr, "%s\n", err)
-		}
-	}()
-	flags := flag.NewFlagSet("", flag.ContinueOnError)
-	flags.SetOutput(stderr)
-	pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
-	runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
-	projectUUID := flags.String("project", "", "project `UUID` for output data")
-	priority := flags.Int("priority", 500, "container request priority")
-	inputFilename := flags.String("i", "-", "input `file`")
-	outputFilename := flags.String("o", "-", "output `file`")
-	maxvariants := flags.Int("max-variants", -1, "drop tiles with more than `N` variants")
-	mincoverage := flags.Float64("min-coverage", 0, "drop tiles with coverage less than `P` across all haplotypes (0 < P ≤ 1)")
-	maxtag := flags.Int("max-tag", -1, "drop tiles with tag ID > `N`")
-	err = flags.Parse(args)
-	if err == flag.ErrHelp {
-		err = nil
-		return 0
-	} else if err != nil {
-		return 2
-	}
-	cmd.output = stdout
-
-	if *pprof != "" {
-		go func() {
-			log.Println(http.ListenAndServe(*pprof, nil))
-		}()
-	}
-
-	if !*runlocal {
-		if *outputFilename != "-" {
-			err = errors.New("cannot specify output file in container mode: not implemented")
-			return 1
-		}
-		runner := arvadosContainerRunner{
-			Name:        "lightning filter",
-			Client:      arvados.NewClientFromEnv(),
-			ProjectUUID: *projectUUID,
-			RAM:         64000000000,
-			VCPUs:       2,
-			Priority:    *priority,
-		}
-		err = runner.TranslatePaths(inputFilename)
-		if err != nil {
-			return 1
-		}
-		runner.Args = []string{"filter", "-local=true",
-			"-i", *inputFilename,
-			"-o", "/mnt/output/library.gob",
-			"-max-variants", fmt.Sprintf("%d", *maxvariants),
-			"-min-coverage", fmt.Sprintf("%f", *mincoverage),
-			"-max-tag", fmt.Sprintf("%d", *maxtag),
-		}
-		var output string
-		output, err = runner.Run()
-		if err != nil {
-			return 1
-		}
-		fmt.Fprintln(stdout, output+"/library.gob")
-		return 0
-	}
-
-	var infile io.ReadCloser
-	if *inputFilename == "-" {
-		infile = ioutil.NopCloser(stdin)
-	} else {
-		infile, err = os.Open(*inputFilename)
-		if err != nil {
-			return 1
-		}
-		defer infile.Close()
-	}
-	log.Print("reading")
-	cgs, err := ReadCompactGenomes(infile)
-	if err != nil {
-		return 1
-	}
-	err = infile.Close()
-	if err != nil {
-		return 1
-	}
-	log.Printf("reading done, %d genomes", len(cgs))
-
-	log.Print("filtering")
-	ntags := 0
-	for _, cg := range cgs {
-		if ntags < len(cg.Variants)/2 {
-			ntags = len(cg.Variants) / 2
-		}
-		if *maxvariants < 0 {
-			continue
-		}
-		maxVariantID := tileVariantID(*maxvariants)
-		for idx, variant := range cg.Variants {
-			if variant > maxVariantID {
-				for _, cg := range cgs {
-					if len(cg.Variants) > idx {
-						cg.Variants[idx & ^1] = 0
-						cg.Variants[idx|1] = 0
-					}
-				}
-			}
-		}
-	}
-
-	if *maxtag >= 0 && ntags > *maxtag {
-		ntags = *maxtag
-		for i, cg := range cgs {
-			if len(cg.Variants) > *maxtag*2 {
-				cgs[i].Variants = cg.Variants[:*maxtag*2]
-			}
-		}
-	}
-
-	if *mincoverage > 0 {
-		mincov := int(*mincoverage * float64(len(cgs)*2))
-		cov := make([]int, ntags)
-		for _, cg := range cgs {
-			for idx, variant := range cg.Variants {
-				if variant > 0 {
-					cov[idx>>1]++
-				}
-			}
-		}
-		for tag, c := range cov {
-			if c < mincov {
-				for _, cg := range cgs {
-					if len(cg.Variants) > tag*2 {
-						cg.Variants[tag*2] = 0
-						cg.Variants[tag*2+1] = 0
-					}
-				}
-			}
-		}
-	}
-
-	log.Print("filtering done")
-
-	var outfile io.WriteCloser
-	if *outputFilename == "-" {
-		outfile = nopCloser{cmd.output}
-	} else {
-		outfile, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0777)
-		if err != nil {
-			return 1
-		}
-		defer outfile.Close()
-	}
-	w := bufio.NewWriter(outfile)
-	enc := gob.NewEncoder(w)
-	log.Print("writing")
-	err = enc.Encode(LibraryEntry{
-		CompactGenomes: cgs,
-	})
-	if err != nil {
-		return 1
-	}
-	log.Print("writing done")
-	err = w.Flush()
-	if err != nil {
-		return 1
-	}
-	err = outfile.Close()
-	if err != nil {
-		return 1
-	}
-	return 0
-}