- make interval operations scale better (#1356)

samtools · May 13, 2019 · ae49710 · ae49710
1 parent 7ce3636
commit ae49710
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Showing 5 changed files with 163 additions and 147 deletions.
diff --git a/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java b/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java
@@ -103,12 +103,12 @@ public SAMSequenceRecord getSequence(final int sequenceIndex) {
     }
 
     /**
-     * @return The index for the given sequence name, or -1 if the name is not found.
+     * @return The index for the given sequence name, or {@value SAMSequenceRecord#UNAVAILABLE_SEQUENCE_INDEX} if the name is not found.
      */
     public int getSequenceIndex(final String sequenceName) {
         final SAMSequenceRecord record = mSequenceMap.get(sequenceName);
         if (record == null) {
-            return -1;
+            return UNAVAILABLE_SEQUENCE_INDEX;
         }
         return record.getSequenceIndex();
     }
@@ -124,11 +124,10 @@ public int size() {
      * @return The sum of the lengths of the sequences in this dictionary
      */
     public long getReferenceLength() {
-        long len = 0L;
-        for (final SAMSequenceRecord seq : getSequences()) {
-            len += seq.getSequenceLength();
-        }
-        return len;
+        return getSequences()
+                .stream()
+                .mapToLong(SAMSequenceRecord::getSequenceLength)
+                .sum();
     }
 
     /**

diff --git a/src/main/java/htsjdk/samtools/SAMSequenceRecord.java b/src/main/java/htsjdk/samtools/SAMSequenceRecord.java
@@ -42,8 +42,9 @@
 public class SAMSequenceRecord extends AbstractSAMHeaderRecord implements Cloneable
 {
     public static final long serialVersionUID = 1L; // AbstractSAMHeaderRecord implements Serializable
+    public final static int UNAVAILABLE_SEQUENCE_INDEX = -1;
     private final String mSequenceName; // Value must be interned() if it's ever set/modified
-    private int mSequenceIndex = -1;
+    private int mSequenceIndex = UNAVAILABLE_SEQUENCE_INDEX;
     private int mSequenceLength = 0;
     public static final String SEQUENCE_NAME_TAG = "SN";
     public static final String SEQUENCE_LENGTH_TAG = "LN";
@@ -196,7 +197,7 @@ public static String truncateSequenceName(final String sequenceName) {
         int truncateAt = sequenceName.length();
         for (final char c : WHITESPACE_CHARS) {
             int index = sequenceName.indexOf(c);
-            if (index != -1 && index < truncateAt) {
+            if (index != UNAVAILABLE_SEQUENCE_INDEX && index < truncateAt) {
                 truncateAt = index;
             }
         }

diff --git a/src/main/java/htsjdk/samtools/util/Interval.java b/src/main/java/htsjdk/samtools/util/Interval.java
@@ -170,12 +170,9 @@ public Interval pad(final int left, final int right) {
      * Counts the total number of bases a collection of intervals.
      */
     public static long countBases(final Collection<Interval> intervals) {
-        long total = 0;
-        for (final Interval i : intervals) {
-            total += i.length();
-        }
-
-        return total;
+        return intervals.stream()
+                .mapToInt(Interval::length)
+                .sum();
     }
 
     /**