From f08fac41090bed842625493c9fa919ee14de865a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 5 Jun 2018 11:25:01 +0100
Subject: [PATCH] JAL-2808 remove duplicated code, tidy case-insensitive
 regexes

---
 src/jalview/io/vcf/VCFLoader.java |   18 ++++--------------
 1 file changed, 4 insertions(+), 14 deletions(-)

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index de2f18a..9438ba9 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -421,8 +421,7 @@ public class VCFLoader
 
   /**
    * Answers true if the field id is matched by any of the filter patterns, else
-   * false. Matching is against regular expression patterns, and is not
-   * case-sensitive.
+   * false. Matching is against non-case-sensitive regular expression patterns.
    * 
    * @param id
    * @param filters
@@ -432,7 +431,7 @@ public class VCFLoader
   {
     for (Pattern p : filters)
     {
-      if (p.matcher(id.toUpperCase()).matches())
+      if (p.matcher(id).matches())
       {
         return true;
       }
@@ -506,8 +505,7 @@ public class VCFLoader
    * Reads the Preference value for the given key, with default specified if no
    * preference set. The value is interpreted as a comma-separated list of
    * regular expressions, and converted into a list of compiled patterns ready
-   * for matching. Patterns are forced to upper-case for non-case-sensitive
-   * matching.
+   * for matching. Patterns are set to non-case-sensitive matching.
    * <p>
    * This supports user-defined filters for fields of interest to capture while
    * processing data. For example, VCF_FIELDS = AF,AC* would mean that VCF INFO
@@ -526,7 +524,7 @@ public class VCFLoader
     {
       try
       {
-      patterns.add(Pattern.compile(token.toUpperCase()));
+        patterns.add(Pattern.compile(token, Pattern.CASE_INSENSITIVE));
       } catch (PatternSyntaxException e)
       {
         System.err.println("Invalid pattern ignored: " + token);
@@ -1190,14 +1188,6 @@ public class VCFLoader
       }
 
       /*
-       * filter out fields we don't want to capture
-       */
-      if (!vcfFieldsOfInterest.contains(key))
-      {
-        continue;
-      }
-
-      /*
        * we extract values for other data which are allele-specific; 
        * these may be per alternate allele (INFO[key].Number = 'A') 
        * or per allele including reference (INFO[key].Number = 'R') 
-- 
1.7.10.2