Add separate map for ID header lines

src/main/java/htsjdk/variant/vcf/VCFHeader.java

@@ -42,6 +42,7 @@
 import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
+import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -75,6 +76,7 @@ public enum HEADER_FIELDS {
     private final Map<String, VCFInfoHeaderLine> mInfoMetaData = new LinkedHashMap<String, VCFInfoHeaderLine>();
     private final Map<String, VCFFormatHeaderLine> mFormatMetaData = new LinkedHashMap<String, VCFFormatHeaderLine>();
     private final Map<String, VCFFilterHeaderLine> mFilterMetaData = new LinkedHashMap<String, VCFFilterHeaderLine>();
+    private final Map<String, Map<String, VCFSimpleHeaderLine>> mIdMetaData = new LinkedHashMap<String, Map<String, VCFSimpleHeaderLine>>();
     private final Map<String, VCFHeaderLine> mOtherMetaData = new LinkedHashMap<String, VCFHeaderLine>();
     private final Map<String, VCFContigHeaderLine> contigMetaData = new LinkedHashMap<>();
 
@@ -374,8 +376,7 @@ private boolean addMetadataLineLookupEntry(final VCFHeaderLine line) {
         } else if ( line instanceof VCFContigHeaderLine ) {
             return addContigMetaDataLineLookupEntry((VCFContigHeaderLine) line);
         } else if ( line instanceof VCFSimpleHeaderLine ){
-            final VCFSimpleHeaderLine simpleLine = (VCFSimpleHeaderLine) line;
-            return addMetaDataLineMapLookupEntry(mOtherMetaData, simpleLine.getKey() + ":" + simpleLine.getID(), simpleLine);
+            return addIdMetaDataLineLookupEntry((VCFSimpleHeaderLine) line);
         } else {
             return addMetaDataLineMapLookupEntry(mOtherMetaData, line.getKey(), line);
         }
@@ -404,6 +405,24 @@ private boolean addContigMetaDataLineLookupEntry(final VCFContigHeaderLine line)
         return true;
     }
 
+    /**
+     * Add a simple header line to the lookup list for ID header lines (mIdMetaData). If there's
+     * already an ID line with the same field type and ID, does not add the line.
+     *
+     * Note: does not add the ID line to the master list of header lines in mMetaData --
+     *       this must be done separately if desired.
+     *
+     * @param line ID header line to add
+     * @return true if line was added to the list of ID lines, otherwise false
+     */
+    private boolean addIdMetaDataLineLookupEntry(final VCFSimpleHeaderLine line) {
+        // Check first layer for key/field type
+        if (!mIdMetaData.containsKey(line.getKey())) {
+            mIdMetaData.put(line.getKey(), new LinkedHashMap<String, VCFSimpleHeaderLine>());
+        }
+        return addMetaDataLineMapLookupEntry(mIdMetaData.get(line.getKey()), line.getID(), line);
+    }
+
     /**
      * Add a header line to the provided map at a given key.  If the key already exists, it will not be replaced.
      * If it does already exist and GeneralUtils.DEBUG_MODE_ENABLED is true, it will issue warnings about duplicates,
@@ -582,32 +601,54 @@ public boolean hasFilterLine(final String id) {
     }
 
     /**
+     * First checks for a VCFHeaderLine with the given key.
+     * If not found, looks for the first ID header line with the given key as the field type.
+     *
      * @param key    the header key name
      * @return the meta data line, or null if there is none
      */
     public VCFHeaderLine getOtherHeaderLine(final String key) {
-        return mOtherMetaData.get(key);
+        if (mOtherMetaData.containsKey(key)) {
+            return mOtherMetaData.get(key);
+        } else if (mIdMetaData.containsKey(key)) {
+            // Get the first item in the linked hash map
+            Map<String, VCFSimpleHeaderLine> fieldMetaData = mIdMetaData.get(key);
+            if (fieldMetaData.keySet().size() > 0) {
+                return fieldMetaData.get(fieldMetaData.keySet().iterator().next());
+            }
+        }
+        return null;
+    }
+
+    /**
+     * Returns the other HeaderLines in their original ordering
+     */
+    public Collection<VCFHeaderLine> getOtherHeaderLines() {
+        return mOtherMetaData.values();
     }
 
     /**
      * @param key    the header key or field type
      * @param id     the header id
      * @return the meta data line, or null if there is none
      */
-    public VCFSimpleHeaderLine getOtherHeaderLine(final String key, final String id) {
-        final VCFHeaderLine line = mOtherMetaData.get(key + ":" + id);
-        if (line instanceof VCFSimpleHeaderLine) {
-            return (VCFSimpleHeaderLine) line;
+    public VCFSimpleHeaderLine getIdHeaderLine(final String key, final String id) {
+        if (mIdMetaData.containsKey(key)) {
+            return mIdMetaData.get(key).get(id);
         } else {
             return null;
         }
     }
 
     /**
-     * Returns the other HeaderLines in their original ordering
+     * Returns the ID HeaderLines, in order by:
+     * - First key/field type to be added
+     * - Within key/field types, in original order
      */
-    public Collection<VCFHeaderLine> getOtherHeaderLines() {
-        return mOtherMetaData.values();
+    public Collection<VCFSimpleHeaderLine> getIdHeaderLines() {
+        final Collection<VCFSimpleHeaderLine> lines = new LinkedList<>();
+        mIdMetaData.forEach((k, v) -> lines.addAll(v.values()));
+        return lines;
     }
 
     /**

src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java

@@ -312,17 +312,17 @@ public void testVCFHeaderAddOtherLine() {
     }
 
     @Test
-    public void testVcfHeaderAddSimpleHeaderLine() {
+    public void testVcfHeaderAddIdHeaderLine() {
         final VCFHeader header = getHiSeqVCFHeader();
         final VCFSimpleHeaderLine delLine = new VCFSimpleHeaderLine("ALT", "DEL", "Deletion relative to the reference");
         final VCFSimpleHeaderLine insLine = new VCFSimpleHeaderLine("ALT", "INS", "Insertion of novel sequence relative to the reference");
         header.addMetaDataLine(delLine);
         header.addMetaDataLine(insLine);
 
-        Assert.assertTrue(header.getOtherHeaderLines().contains(delLine), "DEL line not found in other header lines");
-        Assert.assertTrue(header.getOtherHeaderLines().contains(insLine), "INS line not found in other header lines");
-        Assert.assertNotNull(header.getOtherHeaderLine("ALT", "DEL"), "Lookup for ALT:DEL by key failed");
-        Assert.assertNotNull(header.getOtherHeaderLine("ALT", "INS"), "Lookup for ALT:INS by key failed");
+        Assert.assertTrue(header.getIdHeaderLines().contains(delLine), "DEL line not found in ID header lines");
+        Assert.assertTrue(header.getIdHeaderLines().contains(insLine), "INS line not found in ID header lines");
+        Assert.assertNotNull(header.getIdHeaderLine("ALT", "DEL"), "Lookup for ALT/DEL by key failed");
+        Assert.assertNotNull(header.getIdHeaderLine("ALT", "INS"), "Lookup for ALT/INS by key failed");
     }
 
     @Test
@@ -384,16 +384,16 @@ public void testVCFHeaderAddDuplicateHeaderLine() {
     }
 
     @Test
-    public void testVCFHeaderAddDuplicateSimpleHeaderLine() {
+    public void testVCFHeaderAddDuplicateIdHeaderLine() {
         final VCFHeader header = getHiSeqVCFHeader();
         final VCFSimpleHeaderLine delLine = new VCFSimpleHeaderLine("ALT", "DEL", "Deletion relative to the reference");
         header.addMetaDataLine(delLine);
-        Assert.assertTrue(header.getOtherHeaderLines().contains(delLine), "DEL line not found in other header lines");
+        Assert.assertTrue(header.getIdHeaderLines().contains(delLine), "DEL line not found in ID header lines");
 
-        final int numHeaderLinesBefore = header.getOtherHeaderLines().size();
+        final int numHeaderLinesBefore = header.getIdHeaderLines().size();
         // readd the same header line
         header.addMetaDataLine(delLine);
-        final int numHeaderLinesAfter = header.getOtherHeaderLines().size();
+        final int numHeaderLinesAfter = header.getIdHeaderLines().size();
 
         // assert that we have the same number of other header lines before and after
         Assert.assertEquals(numHeaderLinesBefore, numHeaderLinesAfter);