Merged bugfix

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

@@ -129,7 +129,7 @@ public class CollectSamErrorMetrics extends CommandLineProgram {
             "ERROR:INSERT_LENGTH",
             "ERROR:GC_CONTENT",
             "ERROR:READ_DIRECTION",
-            "ERROR:PAIR_ORIENTATION",
+//            "ERROR:PAIR_ORIENTATION",
             "ERROR:HOMOPOLYMER",
             "ERROR:BINNED_HOMOPOLYMER",
             "ERROR:CYCLE",
@@ -339,8 +339,8 @@ public class CollectSamErrorMetrics extends CommandLineProgram {
                 nTotalLoci++;
 
                 // while there is a next (non-filtered) variant and it is before the locus, advance the pointer.
-                if (checkLocus(vcfFileReader, info.getLocus(), sequenceDictionary)) {
-                    log.debug("Locus does not overlap any variants: " + locusToInterval(info.getLocus(), sequenceDictionary));
+                if (checkLocus(vcfFileReader, info.getLocus())) {
+                    log.debug("Locus does not overlap any variants: " + info.getLocus(), sequenceDictionary);
                     nSkippedLoci++;
                     continue;
                 }
@@ -434,18 +434,16 @@ public class CollectSamErrorMetrics extends CommandLineProgram {
      * HAS SIDE EFFECTS!!! Queries the vcfFileReader
      *
      * @param vcfFileReader      a {@link VCFFileReader} to query for the given locus
-     * @param locus              a {@link Locus} at which to examine the variants
-     * @param sequenceDictionary a dictionary with which to compare the Locatable to the Locus...
+     * @param locusInfo          a {@link SamLocusIterator.LocusInfo} at which to examine the variants
      * @return true if there's a variant over the locus, false otherwise.
      */
-    private static boolean checkLocus(final VCFFileReader vcfFileReader, final Locus locus, final SAMSequenceDictionary sequenceDictionary) {
+    private static boolean checkLocus(final VCFFileReader vcfFileReader, final SamLocusIterator.LocusInfo locusInfo) {
 
         boolean overlaps = false;
-        final Interval queryInterval = locusToInterval(locus, sequenceDictionary);
 
-        if (queryInterval != null) {
+        if (locusInfo != null) {
 
-            try (final CloseableIterator<VariantContext> vcfIterator = vcfFileReader.query(queryInterval)) {
+            try (final CloseableIterator<VariantContext> vcfIterator = vcfFileReader.query(locusInfo)) {
 
                 overlaps = true;
 
@@ -468,22 +466,6 @@ public class CollectSamErrorMetrics extends CommandLineProgram {
         return overlaps;
     }
 
-    /**
-     * Converts the given locus into an interval using the given sequenceDictionary.
-     *
-     * @param locus              The {@link Locus} to convert.
-     * @param sequenceDictionary The {@link SAMSequenceDictionary} to use to convert the given {@code locus}.
-     * @return An {@link Interval} representing the given {@code locus} or {@code null} if it cannot be converted.
-     */
-    private static Interval locusToInterval(final Locus locus, final SAMSequenceDictionary sequenceDictionary) {
-        final SAMSequenceRecord samSequenceRecord = sequenceDictionary.getSequence(locus.getSequenceIndex());
-        if (samSequenceRecord == null) {
-            return null;
-        }
-
-        return new Interval(samSequenceRecord.getSequenceName(), locus.getPosition(), locus.getPosition());
-    }
-
     /**
      * Map of previously seen deletion records, associated with the locus they have been last seen
      */
@@ -697,7 +679,10 @@ public class CollectSamErrorMetrics extends CommandLineProgram {
      */
     private void readFiltersFromFiles() {
         for (final File filterFile : FILTERS) {
-            samErrorReadFilters.add(SamErrorReadFilter.fromFile(filterFile));
+            final SamErrorReadFilter filter = SamErrorReadFilter.fromFile(filterFile);
+            if (filter != null) {
+                samErrorReadFilters.add(filter);
+            }
         }
     }
 

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

@@ -43,7 +43,7 @@ public class IndelErrorMetric extends BaseErrorMetric {
     public long NUM_INSERTED_BASES = 0;
 
     /**
-     * The (phred) rate of insertions. TODO mgatzen Does this make sense?
+     * The (phred) rate of insertions.
      */
     @NoMergingIsDerived
     public int INSERTS_Q = 0;
@@ -61,7 +61,7 @@ public class IndelErrorMetric extends BaseErrorMetric {
     public long NUM_DELETED_BASES = 0;
 
     /**
-     * The (phred) rate of deletions. TODO mgatzen Does this make sense?
+     * The (phred) rate of deletions.
      */
     @NoMergingIsDerived
     public int DELETIONS_Q = 0;

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

@@ -1249,12 +1249,10 @@ public class ReadBaseStratification {
             return null;
         }
         if (operation == CollectSamErrorMetrics.BaseOperation.Insertion && cigarElement.getOperator() != CigarOperator.I) {
-            log.warn("Wrong CIGAR operator for the given position. This is an error and should be fixed.");
-            return null;
+            throw new IllegalStateException("Wrong CIGAR operator for the given position.");
         }
         if (operation == CollectSamErrorMetrics.BaseOperation.Deletion && cigarElement.getOperator() != CigarOperator.D) {
-            log.warn("Wrong CIGAR operator for the given position. This is an error and should be fixed.");
-            return null;
+            throw new IllegalStateException("Wrong CIGAR operator for the given position.");
         }
         return cigarElement.getLength();
     }