Fix input arg in export.

[lightning.git] / exportnumpy.go

diff --git a/exportnumpy.go b/exportnumpy.go
index 78d87af796c4252f0029404f4fa3572c713b6b3a..2c902239f037bb94703ea19851ec6355359c3bc2 100644 (file)
--- a/exportnumpy.go
+++ b/exportnumpy.go
@@ -6,6 +6,7 @@ import (
        "flag"
        "fmt"
        "io"
+       "io/ioutil"
        "log"
        "net/http"
        _ "net/http/pprof"
@@ -29,8 +30,8 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
        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")
-       inputFilename := flags.String("i", "", "input `file`")
-       outputFilename := flags.String("o", "", "output `file`")
+       inputFilename := flags.String("i", "-", "input `file`")
+       outputFilename := flags.String("o", "-", "output `file`")
        err = flags.Parse(args)
        if err == flag.ErrHelp {
                err = nil
@@ -46,7 +47,7 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
        }
 
        if !*runlocal {
-               if *outputFilename != "" {
+               if *outputFilename != "-" {
                        err = errors.New("cannot specify output file in container mode: not implemented")
                        return 1
                }
@@ -69,7 +70,21 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
                return 0
        }
 
-       cgs, err := ReadCompactGenomes(stdin)
+       var input io.ReadCloser
+       if *inputFilename == "-" {
+               input = ioutil.NopCloser(stdin)
+       } else {
+               input, err = os.Open(*inputFilename)
+               if err != nil {
+                       return 1
+               }
+               defer input.Close()
+       }
+       cgs, err := ReadCompactGenomes(input)
+       if err != nil {
+               return 1
+       }
+       err = input.Close()
        if err != nil {
                return 1
        }
@@ -88,7 +103,7 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
        }
 
        var output io.WriteCloser
-       if *outputFilename == "" {
+       if *outputFilename == "-" {
                output = nopCloser{stdout}
        } else {
                output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0777)