-Fixed VCF header line bug

-Added useful trim() method for Strings for characters other than whitespace


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2538 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/Utils.java

@@ -429,6 +429,22 @@ public class Utils {
         return count;
     }
 
+    // trim a string for the given character (i.e. not just whitespace)
+    public static String trim(String str, char ch) {
+        char[] array = str.toCharArray();
+
+
+        int start = 0;
+        while ( start < array.length && array[start] == ch )
+            start++;
+
+        int end = array.length - 1;
+        while ( end > start && array[end] == ch )
+            end--;
+
+        return str.substring(start, end+1);
+    }
+
     public static byte listMaxByte(List<Byte> quals) {
         if (quals.size() == 0) return 0;
         byte m = quals.get(0);

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFFilterHeaderLine.java

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.utils.genotype.vcf;
 
+import org.broadinstitute.sting.utils.Utils;
+
 
 /**
  * @author ebanks
@@ -38,10 +40,10 @@ public class VCFFilterHeaderLine extends VCFHeaderLine {
             throw new IllegalArgumentException("There are too few values in the VCF FILTER header line: " + line);
 
         mName = pieces[0];
-        mDescription = pieces[1];
+        mDescription = Utils.trim(pieces[1], '"');
         // just in case there were some commas in the description
         for (int i = 1; i < pieces.length; i++)
-            mDescription += "," + pieces[i];
+            mDescription += "," + Utils.trim(pieces[i], '"');
     }
 
     protected String makeStringRep() {

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFFormatHeaderLine.java

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.utils.genotype.vcf;
 
+import org.broadinstitute.sting.utils.Utils;
+
 
 /**
  * @author ebanks
@@ -51,10 +53,10 @@ public class VCFFormatHeaderLine extends VCFHeaderLine {
         mName = pieces[0];
         mCount = Integer.valueOf(pieces[1]);
         mType = INFO_TYPE.valueOf(pieces[2]);
-        mDescription = pieces[3];
+        mDescription = Utils.trim(pieces[3], '"');
         // just in case there were some commas in the description
         for (int i = 4; i < pieces.length; i++)
-            mDescription += "," + pieces[i];
+            mDescription += "," + Utils.trim(pieces[i], '"');
     }
 
     protected String makeStringRep() {

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFInfoHeaderLine.java

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.utils.genotype.vcf;
 
+import org.broadinstitute.sting.utils.Utils;
+
 
 /**
  * @author ebanks
@@ -51,10 +53,10 @@ public class VCFInfoHeaderLine extends VCFHeaderLine {
         mName = pieces[0];
         mCount = Integer.valueOf(pieces[1]);
         mType = INFO_TYPE.valueOf(pieces[2]);
-        mDescription = pieces[3];
+        mDescription = Utils.trim(pieces[3], '"');
         // just in case there were some commas in the description
         for (int i = 4; i < pieces.length; i++)
-            mDescription += "," + pieces[i];
+            mDescription += "," + Utils.trim(pieces[i], '"');
     }
 
     protected String makeStringRep() {

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java

@@ -172,9 +172,9 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
                 if ( str.startsWith("##INFO=") )
                     metaData.add(new VCFInfoHeaderLine(str.substring(7)));
                 else if ( str.startsWith("##FILTER=") )
-                    metaData.add(new VCFFilterHeaderLine(str.substring(7)));
+                    metaData.add(new VCFFilterHeaderLine(str.substring(9)));
                 else if ( str.startsWith("##FORMAT=") )
-                    metaData.add(new VCFFormatHeaderLine(str.substring(7)));
+                    metaData.add(new VCFFormatHeaderLine(str.substring(9)));
                 else {
                     int equals = str.indexOf("=");
                     if ( equals != -1 )