From a0b04a3977a19395cf95f3535a9fc6b04c754a3a Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 23 Nov 2017 12:51:15 +0000 Subject: [PATCH] JAL-2808 removed field filters; sort CSQ data by key --- src/jalview/io/vcf/VCFLoader.java | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java index 2847bd7..155e773 100644 --- a/src/jalview/io/vcf/VCFLoader.java +++ b/src/jalview/io/vcf/VCFLoader.java @@ -27,6 +27,8 @@ import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.Map.Entry; +import java.util.SortedMap; +import java.util.TreeMap; import java.util.regex.Pattern; import java.util.regex.PatternSyntaxException; @@ -55,7 +57,7 @@ public class VCFLoader private static final String VCF_FIELDS_PREF = "VCF_FIELDS"; - private static final String DEFAULT_VCF_FIELDS = "AF,AC*"; + private static final String DEFAULT_VCF_FIELDS = ".*"; private static final String DEFAULT_VEP_FIELDS = ".*";// "Allele,Consequence,IMPACT,SWISSPROT,SIFT,PolyPhen,CLIN_SIG"; @@ -915,7 +917,8 @@ public class VCFLoader * inspect CSQ consequences; where possible restrict to the consequence * associated with the current transcript (Feature) */ - Map csqValues = new HashMap<>(); + SortedMap csqValues = new TreeMap<>( + String.CASE_INSENSITIVE_ORDER); for (String consequence : consequences) { -- 1.7.10.2