From: Tom Clegg <tom@tomclegg.ca>
Date: Mon, 23 Nov 2020 02:43:15 +0000 (-0500)
Subject: Propagate -match-chromosome arg to container.
X-Git-Url: https://git.arvados.org/lightning.git/commitdiff_plain/bcacfaf3613014a12b738761e2bf0c0192bbd21a

Propagate -match-chromosome arg to container.

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

diff --git a/import.go b/import.go
index f7e099b4e6..0d2d7379d1 100644
--- a/import.go
+++ b/import.go
@@ -133,6 +133,7 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std
 			fmt.Sprintf("-skip-ooo=%v", cmd.skipOOO),
 			fmt.Sprintf("-output-tiles=%v", cmd.outputTiles),
 			fmt.Sprintf("-save-incomplete-tiles=%v", cmd.saveIncompleteTiles),
+			"-match-chromosome", cmd.matchChromosome.String(),
 			"-output-stats", "/mnt/output/stats.json",
 			"-tag-library", cmd.tagLibraryFile,
 			"-ref", cmd.refFile,