max-tile-size option.

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

diff --git a/annotate.go b/annotate.go
index 2ebe9ce8c9d1b1400bcb26eba86db3c7a2b3c27e..5afc19505ff23a5c14f6f8e1e7cb8b83900d15ef 100644 (file)
--- a/annotate.go
+++ b/annotate.go
@@ -23,6 +23,7 @@ import (
 
 type annotatecmd struct {
        variantHash bool
+       maxTileSize int
 }
 
 func (cmd *annotatecmd) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
@@ -41,6 +42,7 @@ func (cmd *annotatecmd) RunCommand(prog string, args []string, stdin io.Reader,
        inputFilename := flags.String("i", "-", "input `file` (library)")
        outputFilename := flags.String("o", "-", "output `file`")
        flags.BoolVar(&cmd.variantHash, "variant-hash", false, "output variant hash instead of index")
+       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
@@ -71,7 +73,7 @@ func (cmd *annotatecmd) RunCommand(prog string, args []string, stdin io.Reader,
                if err != nil {
                        return 1
                }
-               runner.Args = []string{"annotate", "-local=true", fmt.Sprintf("-variant-hash=%v", cmd.variantHash), "-i", *inputFilename, "-o", "/mnt/output/tilevariants.tsv"}
+               runner.Args = []string{"annotate", "-local=true", fmt.Sprintf("-variant-hash=%v", cmd.variantHash), "-max-tile-size", strconv.Itoa(cmd.maxTileSize), "-i", *inputFilename, "-o", "/mnt/output/tilevariants.tsv"}
                var output string
                output, err = runner.Run()
                if err != nil {
@@ -245,11 +247,11 @@ func (cmd *annotatecmd) exportTileDiffs(outw io.Writer, librdr io.Reader) error
                                                refpart = refseq[refstart : refendtagstart+taglen]
                                                log.Tracef("\n%x tilevar %d,%d endtag %s endtagid %d refendtagstart %d", tv.Blake2b[:13], tag, variant, endtag, endtagid, refendtagstart)
                                        }
-                                       if len(refpart) > 10000 {
+                                       if len(refpart) > cmd.maxTileSize {
                                                log.Warnf("%x tilevar %d,%d skipping long diff, ref %s seq %s ref len %d", tv.Blake2b[:13], tag, variant, refcs.Name, seqname, len(refpart))
                                                continue
                                        }
-                                       if len(tv.Sequence) > 10000 {
+                                       if len(tv.Sequence) > cmd.maxTileSize {
                                                log.Warnf("%x tilevar %d,%d skipping long diff, ref %s seq %s variant len %d", tv.Blake2b[:13], tag, variant, refcs.Name, seqname, len(tv.Sequence))
                                                continue
                                        }