Limit tile size in export.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/export.go b/export.go
index 7ad24cb915091272c45cd2256c3c216a9e7578f3..311ed9ffe68c4422018cc27c571328f0f91d471b 100644 (file)
--- a/export.go
+++ b/export.go
@@ -40,6 +40,7 @@ var (
 
 type exporter struct {
        outputFormat outputFormat
+       maxTileSize  int
 }
 
 func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
@@ -62,6 +63,7 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std
        outputFormatStr := flags.String("output-format", "hgvs", "output `format`: hgvs or vcf")
        outputBed := flags.String("output-bed", "", "also output bed `file`")
        labelsFilename := flags.String("output-labels", "", "also output genome labels csv `file`")
+       flags.IntVar(&cmd.maxTileSize, "max-tile-size", 50000, "don't try to make annotations for tiles bigger than given `size`")
        err = flags.Parse(args)
        if err == flag.ErrHelp {
                err = nil
@@ -117,6 +119,7 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std
                        "-output-format", *outputFormatStr,
                        "-output-bed", *outputBed,
                        "-output-labels", "/mnt/output/labels.csv",
+                       "-max-tile-size", fmt.Sprintf("%d", cmd.maxTileSize),
                        "-i", *inputFilename,
                        "-o", "/mnt/output/export.csv",
                }
@@ -390,12 +393,15 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
                                        // was false during import
                                        continue
                                }
+                               if len(genometile.Sequence) > cmd.maxTileSize {
+                                       continue
+                               }
                                refSequence := reftile.Sequence
                                // If needed, extend the reference
                                // sequence up to the tag at the end
                                // of the genometile sequence.
                                refstepend := refstep + 1
-                               for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genometile.Sequence[len(genometile.Sequence)-taglen:]) {
+                               for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genometile.Sequence[len(genometile.Sequence)-taglen:]) && len(refSequence) <= cmd.maxTileSize {
                                        if &refSequence[0] == &reftile.Sequence[0] {
                                                refSequence = append([]byte(nil), refSequence...)
                                        }