Tell mhapConvert to discard overlaps shorter than minOverlapLength.

marbl · Sep 18, 2020 · b982642 · b982642
1 parent d6b7a1f
commit b982642
Showing 1 changed file with 1 addition and 0 deletions.
diff --git 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";