Make CollectSamErrorMetrics understand lowercased reference (and read) bases

src/main/java/picard/sam/SamErrorMetric/SimpleErrorCalculator.java

@@ -24,16 +24,11 @@
 
 package picard.sam.SamErrorMetric;
 
-import htsjdk.samtools.AlignmentBlock;
-import htsjdk.samtools.Cigar;
-import htsjdk.samtools.CigarElement;
-import htsjdk.samtools.CigarOperator;
 import htsjdk.samtools.reference.SamLocusAndReferenceIterator;
 import htsjdk.samtools.util.AbstractRecordAndOffset;
 import htsjdk.samtools.util.SamLocusIterator;
 import htsjdk.samtools.util.SequenceUtil;
 
-import java.util.List;
 
 /**
  * A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
@@ -50,7 +45,7 @@ public void addBase(final SamLocusIterator.RecordAndOffset recordAndOffset, fina
         super.addBase(recordAndOffset, locusAndRef);
         if (recordAndOffset.getAlignmentType() == AbstractRecordAndOffset.AlignmentType.Match) {
             final byte readBase = recordAndOffset.getReadBase();
-            if (!SequenceUtil.isNoCall(readBase) && (readBase != locusAndRef.getReferenceBase())) {
+            if (!SequenceUtil.isNoCall(readBase) && (!SequenceUtil.basesEqual(readBase, locusAndRef.getReferenceBase()))) {
                 nMismatchingBases++;
             }
         }

src/test/java/picard/sam/SamErrorMetric/BaseErrorCalculationTest.java

@@ -1,7 +1,5 @@
 package picard.sam.SamErrorMetric;
 
-import com.google.common.annotations.VisibleForTesting;
-import com.google.common.collect.Iterables;
 import htsjdk.samtools.*;
 import htsjdk.samtools.reference.ReferenceSequenceFileWalker;
 import htsjdk.samtools.reference.SamLocusAndReferenceIterator;
@@ -14,8 +12,6 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.util.Collection;
-import java.util.HashMap;
 import java.util.List;
 
 /**
@@ -33,7 +29,7 @@ public void testSimpleErrorCalculator() {
         final SAMRecord samRecord = new SAMRecord(samFileHeader);
 
         samRecord.setReadBases("CgTGtGGAcAAAgAAA".getBytes());
-        final byte[] refBases = "CATGGGGAAAAAAAAA".getBytes();
+        final byte[] refBases = "CATGGGGAAAAAAaaa".getBytes();
         final int n = refBases.length;
 
         samRecord.setReadUnmappedFlag(false);

src/test/java/picard/sam/SamErrorMetric/CollectSamErrorMetricsTest.java

@@ -261,10 +261,10 @@ public Object[][] OneCovariateErrorMetricsDataProvider() {
                         new BaseErrorMetric("62A40.2", 72L, 1L)},
                 // No additional mismatches are found on the read with 1 mismatch.
                 {".error_by_mismatches_in_read", simpleSamWithBaseErrors1, priorQ,
-                        new BaseErrorMetric("1", 35L, 0L)},
+                        new BaseErrorMetric("-1", 36L, 0L)},
                 // No additional mismatches are found on the read with 1 mismatch. (Just another way to check)
                 {".error_by_mismatches_in_read", simpleSamWithBaseErrors1, priorQ,
-                        new BaseErrorMetric("0", 37L, 1L)},
+                        new BaseErrorMetric("0", 36L, 1L)},
                 // There should be no errors in the CAG context because it matches reference
                 {".error_by_one_base_padded_context", simpleSamWithBaseErrors1, priorQ,
                         new BaseErrorMetric("CAG", 1L, 0L)},
@@ -400,10 +400,10 @@ public Object[][] oneCovariateIndelErrorMetricsDataProvider() {
                         new BaseErrorMetric("62A40.2", 72L, 1L)},
                 // No additional mismatches are found on the read with 1 mismatch.
                 {".error_by_mismatches_in_read", simpleSamWithBaseErrors1, priorQ,
-                        new BaseErrorMetric("1", 35L, 0L)},
+                        new BaseErrorMetric("-1", 36L, 0L)},
                 // No additional mismatches are found on the read with 1 mismatch. (Just another way to check)
                 {".error_by_mismatches_in_read", simpleSamWithBaseErrors1, priorQ,
-                        new BaseErrorMetric("0", 37L, 1L)},
+                        new BaseErrorMetric("0", 36L, 1L)},
                 // There should be no errors in the CAG context because it matches reference
                 {".error_by_one_base_padded_context", simpleSamWithBaseErrors1, priorQ,
                         new BaseErrorMetric("CAG", 1L, 0L)},
@@ -477,7 +477,7 @@ public void testOneCovariateIndelErrorMetrics(final String errorSubscript, final
                 .stream()
                 .filter(m -> m.COVARIATE.equals(expectedMetric.COVARIATE))
                 .findAny()
-                .orElseThrow(() -> new AssertionError("didn't find metric with COVARIATE==" + expectedMetric.COVARIATE));
+                .orElseThrow(() -> new AssertionError("didn't find metric with COVARIATE==" + expectedMetric.COVARIATE + ": " + (metrics)));
 
         Assert.assertEquals(metric, expectedMetric);
     }

testdata/picard/reference/chrM.reference.fasta

@@ -1,7 +1,7 @@
 >chrM
-GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT
-TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG
-GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT
+gatcacaggtctatcaccctattaaccactcacgggagctctccatgcat
+ttggtattttcgtctggggggtgtgcacgcgatagcattgcgagacgctg
+gagccggagcaccctatgtcgcagtatctgtctttgattcctgcctcatt
 CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA
 AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT
 GTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA
@@ -187,57 +187,57 @@ ACACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCC
 CATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTA
 GCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACT
 AACCAACACACTAACCATATACCAATGGTGGCGCGATGTAACACGAGAAA
-GCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATAC
-GGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTT
-CTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAACTAGGAGGGC
-ACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTC
-CTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCA
-CCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTA
-TTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTAC
-TTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTT
-TGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCC
-TCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACAT
-CACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGT
-TTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTA
-GTATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAA
-AAAAGAGTAATAAACTTCGCCTTAATTTTAATAATCAACACCCTCCTAGC
-CTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACA
-TAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCC
-CGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATT
-ATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAA
-CAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATC
-CTAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAGC
-CGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATT
-ATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTA
-GCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCAT
-ATCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAG
-CTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCT
-ATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCT
-ACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAA
-ACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCAC
-TGACATGACTTTCCAAAAAGCACATAATTTGAATCAACACAACCACCCAC
-AGCCTAATTATTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAA
-CAACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCC
-CCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGC
-CAACGCCACTTATCCAGCGAACCACTATCACGAAAAAAACTCTACCTCTC
-TATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAG
-AACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTG
-GCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCAC
-ATACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCAC
-TAATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACT
-CTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACT
-AGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACT
-TATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTA
-CTTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCAC
-ACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTAC
-TATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACA
-GACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGT
-AGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCA
-TTCTCATAATCGCCCACGGACTCACATCCTCATTACTATTCTGCCTAGCA
-AACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGG
-ACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCC
-TCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCT
-GTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGG
+gcacataccaaggccaccacacaccacctgtccaaaaaggccttcgatac
+gggataatcctatttattacctcagaagtttttttcttcgcaggattttt
+ctgagccttttaccactccagcctagcccctaccccccaactaggagggc
+actggcccccaacaggcatcaccccgctaaatcccctagaagtcccactc
+ctaaacacatccgtattactcgcatcaggagtatcaatcacctgagctca
+ccatagtctaatagaaaacaaccgaaaccaaataattcaagcactgctta
+ttacaattttactgggtctctattttaccctcctacaagcctcagagtac
+ttcgagtctcccttcaccatttccgacggcatctacggctcaacattttt
+tgtagccacaggcttccacggacttcacgtcattattggctcaactttcc
+tcactatctgcttcatccgccaactaatatttcactttacatccaaacat
+cactttggcttcgaagccgccgcctgatactggcattttgtagatgtggt
+ttgactatttctgtatgtctccatctattgatgagggtcttactctttta
+gtataaatagtaccgttaacttccaattaactagttttgacaacattcaa
+aaaagagtaataaacttcgccttaattttaataatcaacaccctcctagc
+cttactactaataattattacattttgactaccacaactcaacggctaca
+tagaaaaatccaccccttacgagtgcggcttcgaccctatatcccccgcc
+cgcgtccctttctccataaaattcttcttagtagctattaccttcttatt
+atttgatctagaaattgccctccttttacccctaccatgagccctacaaa
+caactaacctgccactaatagttatgtcatccctcttattaatcatcatc
+ctagccctaagtctggcctatgagtgactacaaaaaggattagactgagc
+cgaattggtatatagtttaaacaaaacgaatgatttcgactcattaaatt
+atgataatcatatttaccaaatgcccctcatttacataaatattatacta
+gcatttaccatctcacttctaggaatactagtatatcgctcacacctcat
+atcctccctactatgcctagaaggaataatactatcgctgttcattatag
+ctactctcataaccctcaacacccactccctcttagccaatattgtgcct
+attgccatactagtctttgccgcctgcgaagcagcggtgggcctagccct
+actagtctcaatctccaacacatatggcctagactacgtacataacctaa
+acctactccaatgctaaaactaatcgtcccaacaattatattactaccac
+tgacatgactttccaaaaagcacataatttgaatcaacacaaccacccac
+agcctaattattagcatcatccccctactattttttaaccaaatcaacaa
+caacctatttagctgttccccaaccttttcctccgaccccctaacaaccc
+ccctcctaatactaactacctgactcctacccctcacaatcatggcaagc
+caacgccacttatccagcgaaccactatcacgaaaaaaactctacctctc
+tatactaatctccctacaaatctccttaattataacattcacagccacag
+aactaatcatattttatatcttcttcgaaaccacacttatccccaccttg
+gctatcatcacccgatgaggcaaccagccagaacgcctgaacgcaggcac
+atacttcctattctacaccctagtaggctcccttcccctactcatcgcac
+taatttacactcacaacaccctaggctcactaaacattctactactcact
+ctcactgcccaagaactatcaaactcctgagccaacaacttaatatgact
+agcttacacaatagcttttatagtaaagatacctctttacggactccact
+tatgactccctaaagcccatgtcgaagcccccatcgctgggtcaatagta
+cttgccgcagtactcttaaaactaggcggctatggtataatacgcctcac
+actcattctcaaccccctgacaaaacacatagcctaccccttccttgtac
+tatccctatgaggcataattataacaagctccatctgcctacgacaaaca
+gacctaaaatcgctcattgcatactcttcaatcagccacatagccctcgt
+agtaacagccattctcatccaaaccccctgaagcttcaccggcgcagtca
+ttctcataatcgcccacggactcacatcctcattactattctgcctagca
+aactcaaactacgaacgcactcacagtcgcatcataatcctctctcaagg
+acttcaaactctactcccactaatagctttttgatgacttctagcaagcc
+tcgctaacctcgccttaccccccactattaacctactgggagaactctct
+gtgctagtaaccacgttctcctgatcaaatatcactctcctacttacagg
 ACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAA
 CACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTC
 ACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCT