From b9826425676a2eb019fd2ad2f240f2eebd79c35a Mon Sep 17 00:00:00 2001
From: "Brian P. Walenz" <thebri@gmail.com>
Date: Fri, 18 Sep 2020 12:43:09 -0400
Subject: [PATCH] Tell mhapConvert to discard overlaps shorter than
 minOverlapLength.

---
 src/pipelines/canu/OverlapMhap.pm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/pipelines/canu/OverlapMhap.pm b/src/pipelines/canu/OverlapMhap.pm
index 3c1fc4390..396effab7 100644
--- a/src/pipelines/canu/OverlapMhap.pm
+++ b/src/pipelines/canu/OverlapMhap.pm
@@ -480,6 +480,7 @@ sub mhapConfigure ($$$) {
     print F "  \$bin/mhapConvert \\\n";
     print F "    -S ../../$asm.seqStore \\\n";
     print F "    -o ./results/\$qry.mhap.ovb.WORKING \\\n";
+    print F "    -minlength ", getGlobal("minOverlapLength"), " \\\n";
     print F "    \$outPath/\$qry.mhap \\\n";
     print F "  && \\\n";
     print F "  mv ./results/\$qry.mhap.ovb.WORKING ./results/\$qry.mhap.ovb\n";