Accept directories as vcf source args.

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

diff --git a/gvcf2numpy.go b/gvcf2numpy.go
index 890614d1891ad2c5e42f1b6b920a8cdd40df064d..392bd54d2cef8bcd6fef9b6d743bc7cd61341769 100644 (file)
--- a/gvcf2numpy.go
+++ b/gvcf2numpy.go
@@ -8,7 +8,9 @@ import (
        "log"
        "os"
        "os/exec"
+       "path/filepath"
        "runtime"
+       "sort"
        "strings"
        "sync"
 )
@@ -46,6 +48,11 @@ func (cmd *gvcf2numpy) RunCommand(prog string, args []string, stdin io.Reader, s
        }
        cmd.output = stdout
 
+       infiles, err := listVCFFiles(flags.Args())
+       if err != nil {
+               return 1
+       }
+
        log.Printf("tag library %s load starting", cmd.tagLibraryFile)
        f, err := os.Open(cmd.tagLibraryFile)
        if err != nil {
@@ -71,13 +78,50 @@ func (cmd *gvcf2numpy) RunCommand(prog string, args []string, stdin io.Reader, s
        log.Printf("tag library %s load done", cmd.tagLibraryFile)
 
        tilelib := tileLibrary{taglib: &taglib}
-       err = cmd.tileGVCFs(&tilelib, flags.Args())
+       err = cmd.tileGVCFs(&tilelib, infiles)
        if err != nil {
                return 1
        }
        return 0
 }
 
+func listVCFFiles(paths []string) (files []string, err error) {
+       for _, path := range paths {
+               if fi, err := os.Stat(path); err != nil {
+                       return nil, fmt.Errorf("%s: stat failed: %s", path, err)
+               } else if !fi.IsDir() {
+                       files = append(files, path)
+                       continue
+               }
+               d, err := os.Open(path)
+               if err != nil {
+                       return nil, fmt.Errorf("%s: open failed: %s", path, err)
+               }
+               defer d.Close()
+               names, err := d.Readdirnames(0)
+               if err != nil {
+                       return nil, fmt.Errorf("%s: readdir failed: %s", path, err)
+               }
+               sort.Strings(names)
+               for _, name := range names {
+                       if strings.HasSuffix(name, ".vcf") || strings.HasSuffix(name, ".vcf.gz") {
+                               files = append(files, filepath.Join(path, name))
+                       }
+               }
+               d.Close()
+       }
+       for _, file := range files {
+               if _, err := os.Stat(file + ".csi"); err == nil {
+                       continue
+               } else if _, err = os.Stat(file + ".tbi"); err == nil {
+                       continue
+               } else {
+                       return nil, fmt.Errorf("%s: cannot read without .tbi or .csi index file", file)
+               }
+       }
+       return
+}
+
 func (cmd *gvcf2numpy) tileGVCFs(tilelib *tileLibrary, infiles []string) error {
        limit := make(chan bool, runtime.NumCPU())
        errs := make(chan error)