X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/d7b608c2d6ed061bd16e1a18db2638e951883681..dfbfdbd71f01074dedf087cbfee3faa774de3e59:/exportnumpy.go

diff --git a/exportnumpy.go b/exportnumpy.go
index eb15d6d561..27c86a3210 100644
--- a/exportnumpy.go
+++ b/exportnumpy.go
@@ -1,3 +1,7 @@
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
 package lightning
 
 import (
@@ -91,11 +95,9 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
 			"-output-labels", "/mnt/output/labels.csv",
 			"-regions", *regionsFilename,
 			"-expand-regions", fmt.Sprintf("%d", *expandRegions),
-			"-max-variants", fmt.Sprintf("%d", cmd.filter.MaxVariants),
-			"-min-coverage", fmt.Sprintf("%f", cmd.filter.MinCoverage),
-			"-max-tag", fmt.Sprintf("%d", cmd.filter.MaxTag),
 			"-chunks", fmt.Sprintf("%d", *chunks),
 		}
+		runner.Args = append(runner.Args, cmd.filter.Args()...)
 		var output string
 		output, err = runner.Run()
 		if err != nil {
@@ -110,7 +112,7 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
 		retainTileSequences: true,
 		compactGenomes:      map[string][]tileVariantID{},
 	}
-	err = tilelib.LoadDir(context.Background(), *inputDir, nil)
+	err = tilelib.LoadDir(context.Background(), *inputDir)
 	if err != nil {
 		return 1
 	}
@@ -249,19 +251,23 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
 				return
 			}
 			defer f.Close()
-			npw, err := gonpy.NewWriter(f)
+			// gonpy closes our writer and ignores errors. Give it a nopCloser so we can close f properly.
+			npw, err := gonpy.NewWriter(nopCloser{f})
 			if err != nil {
 				lastErr.Store(err)
 				return
 			}
 			npw.Shape = []int{len(names), len(pdis) * 2}
-			npw.WriteInt8(data)
-			// gonpy closes f and ignores errors, doh.
-			// err = f.Close()
-			// if err != nil {
-			// 	lastErr.Store(err)
-			// 	return
-			// }
+			err = npw.WriteInt8(data)
+			if err != nil {
+				lastErr.Store(err)
+				return
+			}
+			err = f.Close()
+			if err != nil {
+				lastErr.Store(err)
+				return
+			}
 		}()
 	}
 	wg.Wait()
@@ -357,7 +363,7 @@ func lowqual(tilelib *tileLibrary) (lowqual []map[tileVariantID]bool) {
 	for tag, variants := range tilelib.variant {
 		lq := lowqual[tag]
 		for varidx, hash := range variants {
-			if len(tilelib.seq[hash]) == 0 {
+			if len(tilelib.hashSequence(hash)) == 0 {
 				if lq == nil {
 					lq = map[tileVariantID]bool{}
 					lowqual[tag] = lq
@@ -398,22 +404,20 @@ func cgs2array(tilelib *tileLibrary, names []string, lowqual []map[tileVariantID
 	return
 }
 
-func chooseTiles(tilelib *tileLibrary, regionsFilename string, expandRegions int) (drop []bool, err error) {
-	if regionsFilename == "" {
-		return
-	}
+func makeMask(regionsFilename string, expandRegions int) (*mask, error) {
+	log.Printf("makeMask: reading %s", regionsFilename)
 	rfile, err := zopen(regionsFilename)
 	if err != nil {
-		return
+		return nil, err
 	}
 	defer rfile.Close()
-	regions, err := ioutil.ReadAll(rfile)
+	regions, err := io.ReadAll(rfile)
 	if err != nil {
-		return
+		return nil, err
 	}
 
-	log.Print("chooseTiles: building mask")
-	mask := &mask{}
+	log.Print("makeMask: building mask")
+	var mask mask
 	for _, line := range bytes.Split(regions, []byte{'\n'}) {
 		if bytes.HasPrefix(line, []byte{'#'}) {
 			continue
@@ -437,14 +441,24 @@ func chooseTiles(tilelib *tileLibrary, regionsFilename string, expandRegions int
 				// GFF/GTF
 				end++
 			} else {
-				err = fmt.Errorf("cannot parse input line as BED or GFF/GTF: %q", line)
-				return
+				return nil, fmt.Errorf("cannot parse input line as BED or GFF/GTF: %q", line)
 			}
 		}
 		mask.Add(refseqname, start-expandRegions, end+expandRegions)
 	}
-	log.Print("chooseTiles: mask.Freeze")
+	log.Print("makeMask: mask.Freeze")
 	mask.Freeze()
+	return &mask, nil
+}
+
+func chooseTiles(tilelib *tileLibrary, regionsFilename string, expandRegions int) (drop []bool, err error) {
+	if regionsFilename == "" {
+		return
+	}
+	mask, err := makeMask(regionsFilename, expandRegions)
+	if err != nil {
+		return
+	}
 
 	tagset := tilelib.taglib.Tags()
 	if len(tagset) == 0 {