Gzip gob files.

[lightning.git] / export.go

diff --git a/export.go b/export.go
index 739f8efa1295d6c06176f3f3ebfe9c7cf0ccad77..b6b160ddb79311fe3a5964b25e2ca0efe482abdc 100644 (file)
--- a/export.go
+++ b/export.go
@@ -132,9 +132,9 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std
        var mtx sync.Mutex
        var cgs []CompactGenome
        tilelib := tileLibrary{
-               includeNoCalls: true,
+               retainNoCalls: true,
        }
-       err = tilelib.LoadGob(context.Background(), input, func(cg CompactGenome) {
+       err = tilelib.LoadGob(context.Background(), input, strings.HasSuffix(*inputFilename, ".gz"), func(cg CompactGenome) {
                if *pick != "" && *pick != cg.Name {
                        return
                }
@@ -188,7 +188,7 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std
                bedbufw = bufio.NewWriter(bedout)
        }
 
-       err = cmd.export(bufw, bedout, input, tilelib.taglib.keylen, refseq, cgs)
+       err = cmd.export(bufw, bedout, input, strings.HasSuffix(*inputFilename, ".gz"), tilelib.taglib.keylen, refseq, cgs)
        if err != nil {
                return 1
        }
@@ -217,7 +217,7 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std
        return 0
 }
 
-func (cmd *exporter) export(out, bedout io.Writer, librdr io.Reader, taglen int, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
+func (cmd *exporter) export(out, bedout io.Writer, librdr io.Reader, gz bool, taglen int, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
        need := map[tileLibRef]bool{}
        var seqnames []string
        for seqname, librefs := range refseq {
@@ -242,7 +242,7 @@ func (cmd *exporter) export(out, bedout io.Writer, librdr io.Reader, taglen int,
 
        log.Infof("export: loading %d tile variants", len(need))
        tileVariant := map[tileLibRef]TileVariant{}
-       err := DecodeLibrary(librdr, func(ent *LibraryEntry) error {
+       err := DecodeLibrary(librdr, gz, func(ent *LibraryEntry) error {
                for _, tv := range ent.TileVariants {
                        libref := tileLibRef{Tag: tv.Tag, Variant: tv.Variant}
                        if need[libref] {
@@ -332,10 +332,16 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
                                        continue
                                }
                                tagcoverage++
-                               genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
                                if variant == libref.Variant {
                                        continue
                                }
+                               genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
+                               if len(genometile.Sequence) == 0 {
+                                       // Hash is known but sequence
+                                       // is not, e.g., retainNoCalls
+                                       // was false during import
+                                       continue
+                               }
                                refSequence := reftile.Sequence
                                // If needed, extend the reference
                                // sequence up to the tag at the end