Yf add unknown so

src/main/java/htsjdk/samtools/SAMFileHeader.java

@@ -24,6 +24,8 @@
 package htsjdk.samtools;
 
 
+import htsjdk.samtools.util.CollectionUtil;
+import htsjdk.samtools.util.Log;
 import htsjdk.samtools.util.StringLineReader;
 
 import java.io.StringWriter;
@@ -47,14 +49,17 @@
     public static final String SORT_ORDER_TAG = "SO";
     public static final String GROUP_ORDER_TAG = "GO";
     public static final String CURRENT_VERSION = "1.5";
-    public static final Set<String> ACCEPTABLE_VERSIONS =
-            new HashSet<String>(Arrays.asList("1.0", "1.3", "1.4", "1.5"));
+    public static final Set<String> ACCEPTABLE_VERSIONS = CollectionUtil.makeSet("1.0", "1.3", "1.4", "1.5");
 
+    private SortOrder sortOrder = null;
+    private GroupOrder groupOrder = null;
+
+    private static final Log log = Log.getInstance(SAMFileHeader.class);
     /**
      * These tags are of known type, so don't need a type field in the text representation.
      */
     public static final Set<String> STANDARD_TAGS =
-            new HashSet<String>(Arrays.asList(VERSION_TAG, SORT_ORDER_TAG, GROUP_ORDER_TAG));
+            new HashSet<>(Arrays.asList(VERSION_TAG, SORT_ORDER_TAG, GROUP_ORDER_TAG));
 
     @Override
     Set<String> getStandardTags() {
@@ -65,11 +70,11 @@
      * Ways in which a SAM or BAM may be sorted.
      */
     public enum SortOrder {
-
         unsorted(null),
         queryname(SAMRecordQueryNameComparator.class),
         coordinate(SAMRecordCoordinateComparator.class),
-        duplicate(SAMRecordDuplicateComparator.class); // NB: this is not in the SAM spec!
+        duplicate(SAMRecordDuplicateComparator.class), // NB: this is not in the SAM spec!
+        unknown(null);
 
         private final Class<? extends SAMRecordComparator> comparator;
 
@@ -106,16 +111,14 @@ public SAMRecordComparator getComparatorInstance() {
         none, query, reference
     }
 
-    private List<SAMReadGroupRecord> mReadGroups =
-        new ArrayList<SAMReadGroupRecord>();
-    private List<SAMProgramRecord> mProgramRecords = new ArrayList<SAMProgramRecord>();
-    private final Map<String, SAMReadGroupRecord> mReadGroupMap =
-        new HashMap<String, SAMReadGroupRecord>();
-    private final Map<String, SAMProgramRecord> mProgramRecordMap = new HashMap<String, SAMProgramRecord>();
+    private List<SAMReadGroupRecord> mReadGroups = new ArrayList<>();
+    private List<SAMProgramRecord> mProgramRecords = new ArrayList<>();
+    private final Map<String, SAMReadGroupRecord> mReadGroupMap = new HashMap<>();
+    private final Map<String, SAMProgramRecord> mProgramRecordMap = new HashMap<>();
     private SAMSequenceDictionary mSequenceDictionary = new SAMSequenceDictionary();
-    final private List<String> mComments = new ArrayList<String>();
+    final private List<String> mComments = new ArrayList<>();
     private String textHeader;
-    private final List<SAMValidationError> mValidationErrors = new ArrayList<SAMValidationError>();
+    private final List<SAMValidationError> mValidationErrors = new ArrayList<>();
 
     public SAMFileHeader() {
         setAttribute(VERSION_TAG, CURRENT_VERSION);
@@ -128,11 +131,11 @@ public SAMFileHeader(final SAMSequenceDictionary dict) {
     }
 
     public String getVersion() {
-        return (String) getAttribute("VN");
+        return getAttribute(VERSION_TAG);
     }
 
     public String getCreator() {
-        return (String) getAttribute("CR");
+        return getAttribute("CR");
     }
 
     public SAMSequenceDictionary getSequenceDictionary() {
@@ -249,26 +252,47 @@ public SAMProgramRecord createProgramRecord() {
     }
 
     public SortOrder getSortOrder() {
-        final String so = getAttribute("SO");
-        if (so == null || so.equals("unknown")) {
-            return SortOrder.unsorted;
+        if (sortOrder == null) {
+            final String so = getAttribute(SORT_ORDER_TAG);
+            if (so == null) {
+                sortOrder = SortOrder.unsorted;
+            } else {
+                try {
+                    return SortOrder.valueOf(so);
+                } catch (IllegalArgumentException e) {
+                    log.warn("Found non conforming header SO tag: " + so + ". Treating as 'unknown'.");
+                    sortOrder = SortOrder.unknown;
+                }
+            }
         }
-        return SortOrder.valueOf((String) so);
+        return sortOrder;
     }
 
     public void setSortOrder(final SortOrder so) {
-        setAttribute("SO", so.name());
+        sortOrder = so;
+        setAttribute(SORT_ORDER_TAG, so.name());
     }
 
     public GroupOrder getGroupOrder() {
-        if (getAttribute("GO") == null) {
-            return GroupOrder.none;
+        if (groupOrder == null) {
+            final String go = getAttribute(GROUP_ORDER_TAG);
+            if (go == null) {
+                groupOrder = GroupOrder.none;
+            } else {
+                try {
+                    return GroupOrder.valueOf(go);
+                } catch (IllegalArgumentException e) {
+                    log.warn("Found non conforming header GO tag: " + go + ". Treating as 'none'.");
+                    groupOrder = GroupOrder.none;
+                }
+            }
         }
-        return GroupOrder.valueOf((String)getAttribute("GO"));
+        return groupOrder;
     }
 
     public void setGroupOrder(final GroupOrder go) {
-        setAttribute("GO", go.name());
+        groupOrder = go;
+        setAttribute(GROUP_ORDER_TAG, go.name());
     }
 
     /**
@@ -372,7 +396,7 @@ public String getSAMString() {
     public static class PgIdGenerator {
         private int recordCounter;
 
-        private final Set<String> idsThatAreAlreadyTaken = new HashSet<String>();
+        private final Set<String> idsThatAreAlreadyTaken = new HashSet<>();
 
         public PgIdGenerator(final SAMFileHeader header) {
             for (final SAMProgramRecord pgRecord : header.getProgramRecords()) {
@@ -400,7 +424,6 @@ public String getNonCollidingId(final String recordId) {
                 idsThatAreAlreadyTaken.add(newId);
                 return newId;
             }
-
         }
     }
 }

src/main/java/htsjdk/samtools/SAMTextHeaderCodec.java

@@ -228,6 +228,25 @@ private void parseHDLine(final ParsedHeaderLine parsedHeaderLine) {
         if (!parsedHeaderLine.requireTag(SAMFileHeader.VERSION_TAG)) {
             return;
         }
+
+        final String soString = parsedHeaderLine.getValue(SAMFileHeader.SORT_ORDER_TAG);
+        try {
+            if (soString != null) SAMFileHeader.SortOrder.valueOf(soString);
+        } catch (IllegalArgumentException e) {
+            reportErrorParsingLine(HEADER_LINE_START + parsedHeaderLine.getHeaderRecordType() +
+                            " line has non-conforming SO tag value: "+ soString + ".",
+                    SAMValidationError.Type.HEADER_TAG_NON_CONFORMING_VALUE, null);
+        }
+
+        final String goString = parsedHeaderLine.getValue(SAMFileHeader.GROUP_ORDER_TAG);
+        try {
+            if (goString != null) SAMFileHeader.GroupOrder.valueOf(goString);
+        } catch (IllegalArgumentException e) {
+            reportErrorParsingLine(HEADER_LINE_START + parsedHeaderLine.getHeaderRecordType() +
+                            " line has non-conforming GO tag value: "+ goString + ".",
+                    SAMValidationError.Type.HEADER_TAG_NON_CONFORMING_VALUE, null);
+        }
+
         transferAttributes(mFileHeader, parsedHeaderLine.mKeyValuePairs);
     }
 

src/main/java/htsjdk/samtools/SAMValidationError.java

@@ -171,6 +171,9 @@
 
         HEADER_RECORD_MISSING_REQUIRED_TAG,
 
+        /** Header tag contains illegal value */
+        HEADER_TAG_NON_CONFORMING_VALUE,
+
         /** Date string is not ISO-8601 */
         INVALID_DATE_STRING(Severity.WARNING),
 

src/test/java/htsjdk/samtools/ValidateSamFileTest.java

@@ -499,10 +499,24 @@ public void duplicateReadsOutOfOrder() throws Exception {
                         "@RG\tID:0\tSM:Hi,Mom!\n" +
                         "E\t147\tchr1\t15\t255\t10M\t=\t2\t-30\tCAACAGAAGC\t)'.*.+2,))\tU2:Z:CAA";
 
+        final String SOTagCorrectlyProcessTestData =
+                "@HD\tVN:1.0\tSO:NOTKNOWN\n" +
+                        "@SQ\tSN:chr1\tLN:101\n" +
+                        "@RG\tID:0\tSM:Hi,Mom!\n" +
+                        "E\t147\tchr1\t15\t255\t10M\t=\t2\t-30\tCAACAGAAGC\t)'.*.+2,))\tU2:Z:CAA";
+
+        final String GOTagCorrectlyProcessTestData =
+                "@HD\tVN:1.0\tGO:NOTKNOWN\n" +
+                        "@SQ\tSN:chr1\tLN:101\n" +
+                        "@RG\tID:0\tSM:Hi,Mom!\n" +
+                        "E\t147\tchr1\t15\t255\t10M\t=\t2\t-30\tCAACAGAAGC\t)'.*.+2,))\tU2:Z:CAA";
+
         return new Object[][]{
                 {E2TagCorrectlyProcessTestData.getBytes(), SAMValidationError.Type.E2_BASE_EQUALS_PRIMARY_BASE},
                 {E2TagCorrectlyProcessTestData.getBytes(), SAMValidationError.Type.MISMATCH_READ_LENGTH_AND_E2_LENGTH},
-                {U2TagCorrectlyProcessTestData.getBytes(), SAMValidationError.Type.MISMATCH_READ_LENGTH_AND_U2_LENGTH}
+                {U2TagCorrectlyProcessTestData.getBytes(), SAMValidationError.Type.MISMATCH_READ_LENGTH_AND_U2_LENGTH},
+                {SOTagCorrectlyProcessTestData.getBytes(), SAMValidationError.Type.HEADER_TAG_NON_CONFORMING_VALUE},
+                {GOTagCorrectlyProcessTestData.getBytes(), SAMValidationError.Type.HEADER_TAG_NON_CONFORMING_VALUE}
         };
     }
 

src/test/java/htsjdk/samtools/cram/lossy/QualityScorePreservationTest.java

@@ -97,12 +97,10 @@ public void test2() {
         }
     }
 
-    private SAMFileHeader samFileHeader = new SAMFileHeader();
-
     private SAMRecord buildSAMRecord(String seqName, String line) {
         ByteArrayOutputStream baos = new ByteArrayOutputStream();
         try {
-            baos.write("@HD\tVN:1.0\tGO:none SO:coordinate\n".getBytes());
+            baos.write("@HD\tVN:1.0\tGO:none\tSO:coordinate\n".getBytes());
             baos.write(("@SQ\tSN:" + seqName + "\tLN:247249719\n").getBytes());
             baos.write(line.replaceAll("\\s+", "\t").getBytes());
             baos.close();