Don't require reference data when all inputs are fasta.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

diff --git a/import.go b/import.go
index 2f9888ce390427c0b426756f936d6c1df338c180..a38abc6861aaecf593c3e987a6036470d8ae43bc 100644 (file)
--- a/import.go
+++ b/import.go
@@ -4,6 +4,7 @@ import (
        "bufio"
        "compress/gzip"
        "encoding/gob"
+       "errors"
        "flag"
        "fmt"
        "io"
@@ -46,8 +47,8 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std
                return 0
        } else if err != nil {
                return 2
-       } else if cmd.refFile == "" || cmd.tagLibraryFile == "" {
-               fmt.Fprintln(os.Stderr, "cannot run without -tag-library and -ref arguments")
+       } else if cmd.tagLibraryFile == "" {
+               fmt.Fprintln(os.Stderr, "cannot import without -tag-library argument")
                return 2
        } else if flags.NArg() == 0 {
                flags.Usage()
@@ -76,7 +77,7 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std
        }()
        w := bufio.NewWriter(stdout)
        cmd.encoder = gob.NewEncoder(w)
-       err = cmd.tileGVCFs(tilelib, infiles)
+       err = cmd.tileInputs(tilelib, infiles)
        if err != nil {
                return 1
        }
@@ -174,7 +175,7 @@ func listInputFiles(paths []string) (files []string, err error) {
        return
 }
 
-func (cmd *importer) tileGVCFs(tilelib *tileLibrary, infiles []string) error {
+func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
        starttime := time.Now()
        errs := make(chan error, 1)
        todo := make(chan func() error, len(infiles)*2)
@@ -275,6 +276,10 @@ func (cmd *importer) tileGVCFs(tilelib *tileLibrary, infiles []string) error {
 }
 
 func (cmd *importer) tileGVCF(tilelib *tileLibrary, infile string, phase int) (tileseq tileSeq, err error) {
+       if cmd.refFile == "" {
+               err = errors.New("cannot import vcf: reference data (-ref) not specified")
+               return
+       }
        args := []string{"bcftools", "consensus", "--fasta-ref", cmd.refFile, "-H", fmt.Sprint(phase + 1), infile}
        indexsuffix := ".tbi"
        if _, err := os.Stat(infile + ".csi"); err == nil {