Configurable chromosome name pattern.

[lightning.git] / import.go

diff --git a/import.go b/import.go
index 629fccac2fc049646a58c23fbbbd11a14292ef52..f7e099b4e6718509514f28dfec911157a5c5ddbe 100644 (file)
--- a/import.go
+++ b/import.go
@@ -41,6 +41,7 @@ type importer struct {
        outputTiles         bool
        saveIncompleteTiles bool
        outputStats         string
+       matchChromosome     *regexp.Regexp
        encoder             *gob.Encoder
 }
 
@@ -62,6 +63,7 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std
        flags.BoolVar(&cmd.outputTiles, "output-tiles", false, "include tile variant sequences in output file")
        flags.BoolVar(&cmd.saveIncompleteTiles, "save-incomplete-tiles", false, "treat tiles with no-calls as regular tiles")
        flags.StringVar(&cmd.outputStats, "output-stats", "", "output stats to `file` (json)")
+       matchChromosome := flags.String("match-chromosome", "^(chr)?([0-9]+|X|Y|MT?)$", "import chromosomes that match the given `regexp`")
        priority := flags.Int("priority", 500, "container request priority")
        pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
        loglevel := flags.String("loglevel", "info", "logging threshold (trace, debug, info, warn, error, fatal, or panic)")
@@ -91,6 +93,11 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std
        }
        log.SetLevel(lvl)
 
+       cmd.matchChromosome, err = regexp.Compile(*matchChromosome)
+       if err != nil {
+               return 1
+       }
+
        if !cmd.runLocal {
                runner := arvadosContainerRunner{
                        Name:        "lightning import",
@@ -214,7 +221,7 @@ func (cmd *importer) tileFasta(tilelib *tileLibrary, infile string) (tileSeq, []
                }
                defer input.Close()
        }
-       return tilelib.TileFasta(infile, input)
+       return tilelib.TileFasta(infile, input, cmd.matchChromosome)
 }
 
 func (cmd *importer) loadTagLibrary() (*tagLibrary, error) {
@@ -480,7 +487,7 @@ func (cmd *importer) tileGVCF(tilelib *tileLibrary, infile string, phase int) (t
                return
        }
        defer consensus.Wait()
-       tileseq, stats, err = tilelib.TileFasta(fmt.Sprintf("%s phase %d", infile, phase+1), stdout)
+       tileseq, stats, err = tilelib.TileFasta(fmt.Sprintf("%s phase %d", infile, phase+1), stdout, cmd.matchChromosome)
        if err != nil {
                return
        }