Fix for issue #513: NPE in ValidateSamFile with CRAM

src/main/java/htsjdk/samtools/SamFileValidator.java

@@ -1,7 +1,7 @@
 /*
  * The MIT License
  *
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2009-2016 The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -286,8 +286,7 @@ private void validateSamRecordsAndQualityFormat(final Iterable<SAMRecord> samRec
                 if (cigarIsValid) {
                     try {
                         validateNmTag(record, recordNumber);
-                    }
-                    catch (SAMException e) {
+                    } catch (SAMException e) {
                         if (hasValidSortOrder) {
                             // If a CRAM file has an invalid sort order, the ReferenceFileWalker will throw a
                             // SAMException due to an out of order request when retrieving reference bases during NM
@@ -539,12 +538,12 @@ private void validateHeader(final SAMFileHeader fileHeader) {
                         "A platform (PL) attribute was not found for read group ",
                         readGroupID));
             }
-            else { 
+            else {
                 // NB: cannot be null, so not catching a NPE
                 try {
                     SAMReadGroupRecord.PlatformValue.valueOf(platformValue.toUpperCase());
                 } catch (IllegalArgumentException e) {
-                    addError(new SAMValidationError(Type.INVALID_PLATFORM_VALUE, 
+                    addError(new SAMValidationError(Type.INVALID_PLATFORM_VALUE,
                             "The platform (PL) attribute (" + platformValue + ") + was not one of the valid values for read group ",
                             readGroupID));
                 }

src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileWalker.java

@@ -1,7 +1,7 @@
 /*
  * The MIT License
  *
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2009-2016 The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -83,7 +83,7 @@ public ReferenceSequence get(final int sequenceIndex) {
         }
         referenceSequence = null;
 
-        if(referenceSequenceFile.isIndexed()) {
+        if(referenceSequenceFile.isIndexed() && referenceSequenceFile.getSequenceDictionary() != null) {
             final SAMSequenceRecord samSequenceRecord = referenceSequenceFile.getSequenceDictionary().getSequence(sequenceIndex);
             if(samSequenceRecord != null) {
                 referenceSequence = referenceSequenceFile.getSequence(samSequenceRecord.getSequenceName()) ;

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

@@ -1,7 +1,7 @@
 /*
  * The MIT License
  *
- * Copyright (c) 2009 The Broad Institute
+ * Copyright (c) 2009-2016 The Broad Institute
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -27,6 +27,7 @@
 import htsjdk.samtools.BamIndexValidator.IndexValidationStringency;
 import htsjdk.samtools.metrics.MetricBase;
 import htsjdk.samtools.metrics.MetricsFile;
+import htsjdk.samtools.reference.FastaSequenceFile;
 import htsjdk.samtools.reference.ReferenceSequence;
 import htsjdk.samtools.reference.ReferenceSequenceFile;
 import htsjdk.samtools.util.CloserUtil;
@@ -64,6 +65,20 @@ public void testValidSamFile() throws Exception {
     }
 
     @Test
+    public void testValidCRAMFileWithoutSeqDict() throws Exception {
+        final File reference = new File(TEST_DATA_DIR, "nm_tag_validation.fa");
+        final SamReader samReader = SamReaderFactory
+                .makeDefault()
+                .validationStringency(ValidationStringency.SILENT)
+                .referenceSequence(reference)
+                .open(new File(TEST_DATA_DIR, "nm_tag_validation.cram"));
+        final Histogram<String> results = executeValidation(samReader,
+                new FastaSequenceFile(reference, true),
+                IndexValidationStringency.EXHAUSTIVE);
+        Assert.assertTrue(!results.isEmpty());
+    }
+
+    @Test
     public void testSamFileVersion1pt5() throws Exception {
         final SamReader samReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(new File(TEST_DATA_DIR, "test_samfile_version_1pt5.bam"));
         final Histogram<String> results = executeValidation(samReader, null, IndexValidationStringency.EXHAUSTIVE);
@@ -231,26 +246,32 @@ public void testNmFlagValidation() throws IOException {
         final Histogram<String> results = executeValidation(samBuilder.getSamReader(), new ReferenceSequenceFile() {
             private int index = 0;
 
+            @Override
             public SAMSequenceDictionary getSequenceDictionary() {
                 return null;
             }
 
+            @Override
             public ReferenceSequence nextSequence() {
                 final byte[] bases = new byte[10000];
                 Arrays.fill(bases, (byte) 'A');
                 return new ReferenceSequence("foo", index++, bases);
             }
 
+            @Override
             public void reset() {
                 this.index = 0;
             }
 
+            @Override
             public boolean isIndexed() { return false; }
 
+            @Override
             public ReferenceSequence getSequence(final String contig) {
                 throw new UnsupportedOperationException();
             }
 
+            @Override
             public ReferenceSequence getSubsequenceAt(final String contig, final long start, final long stop) {
                 throw new UnsupportedOperationException();
             }

src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.fa

@@ -0,0 +1,71 @@
+>17 17:1-4200
+AAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAA
+TGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGA
+GCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAA
+GACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACAC
+GCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACA
+GTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGA
+AAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATA
+AATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAG
+GAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATC
+ACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTG
+TGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACAT
+GCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGG
+CAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGA
+AAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATATTCTCTGTGTTGA
+TTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTAC
+CAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAG
+TGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCG
+CCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAA
+GAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGAC
+CAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGT
+TCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTC
+CCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGAC
+GCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCC
+CGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTA
+GGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGA
+GCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTT
+TGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCAGC
+CACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAG
+CGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCA
+CTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCC
+TGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGG
+TCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACA
+GTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGC
+CAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCAC
+GGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGC
+AGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGC
+ACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCG
+GCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAG
+CTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATC
+GTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAA
+AAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGG
+AGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCG
+CATCACTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTCTCAAAAAAGAAAGGAAGAA
+ATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGG
+CCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCT
+CTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTAT
+TTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGG
+ACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATG
+TGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCT
+TTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAG
+CAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTG
+CCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAG
+ACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGG
+GCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTA
+ATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCA
+GCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTG
+GCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGG
+GAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGT
+AAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCC
+TGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAACATATAT
+ATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTG
+TTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTAC
+ACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGC
+CTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCG
+TCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCAT
+GCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAT
+GGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACCCGCT
+ACACTCCTTCTTAGGGCTGATATTCCACGCACCCGCTACACTCCTTCTTAGGGCTGATAT
+TCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTT
+CTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCAC

src/test/resources/htsjdk/samtools/ValidateSamFileTest/nm_tag_validation.fa.fai

@@ -0,0 +1 @@
+17	4200	14	60	61