From a3b1762ac59e43ed1bc777ac7654740e3fe5879c Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Thu, 9 Apr 2020 16:58:32 +0100 Subject: [PATCH 1/2] revert to doing samtools amplicon-clip (AKA primer clip)a by default for markdup_method none. --- data/vtlib/markdup_none.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/vtlib/markdup_none.json b/data/vtlib/markdup_none.json index 7235fdf6d..632f8447e 100644 --- a/data/vtlib/markdup_none.json +++ b/data/vtlib/markdup_none.json @@ -14,7 +14,7 @@ "use_STDIN": true, "use_STDOUT": true, "cmd":{ - "select":"primer_clip_method", "select_range":[1], "default":"no_clip", + "select":"primer_clip_method", "select_range":[1], "default":"samtools", "cases":{ "samtools":[ {"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "amplicon-clip", From 8feaac45cbb8f6750e08be1ce295ddfe82d751be Mon Sep 17 00:00:00 2001 From: mgcam Date: Thu, 9 Apr 2020 17:09:33 +0100 Subject: [PATCH 2/2] Changes file tweak --- Changes | 1 - 1 file changed, 1 deletion(-) diff --git a/Changes b/Changes index b316b928d..a29af1a4d 100644 --- a/Changes +++ b/Changes @@ -4,7 +4,6 @@ CHANGES LOG 0.28.0 - a new template for cases when marking duplicates is not required, with an option to clip primers, which relies on a new feature in samtools - and is not enabled by default 0.27.0 - check for divide by 0 when calc samtools subsample value