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JAL-2808 removed field filters; sort CSQ data by key
[jalview.git]
/
src
/
jalview
/
io
/
vcf
/
VCFLoader.java
diff --git
a/src/jalview/io/vcf/VCFLoader.java
b/src/jalview/io/vcf/VCFLoader.java
index
2847bd7
..
155e773
100644
(file)
--- 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.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;
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 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";
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)
*/
* inspect CSQ consequences; where possible restrict to the consequence
* associated with the current transcript (Feature)
*/
- Map<String, String> csqValues = new HashMap<>();
+ SortedMap<String, String> csqValues = new TreeMap<>(
+ String.CASE_INSENSITIVE_ORDER);
for (String consequence : consequences)
{
for (String consequence : consequences)
{