From 1e00b33b284c009e6480b384b1c4772a9233d865 Mon Sep 17 00:00:00 2001 From: Dominika Maziec Date: Mon, 12 Oct 2020 09:38:54 +0200 Subject: [PATCH] Freebayes sorted variants --- core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala b/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala index 401baec..1cae6e2 100644 --- a/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala +++ b/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala @@ -113,9 +113,8 @@ class Freebayes( alignments.pipe[VariantContext, VariantContextProduct, VariantContextDataset, BAMInFormatter]( cmd = builder.build(), files = builder.getFiles() - ) - - // val headerLines = accumulator.value.distinct - // variantContexts.replaceHeaderLines(headerLines) + ).sort() + val headerLines = accumulator.value.distinct + variantContexts.replaceHeaderLines(headerLines) } }