From e4c8c0d42aae2e02b70dec7f630f41edce6af860 Mon Sep 17 00:00:00 2001
From: Denis Verkhoturov <denis_verkhoturov@epam.com>
Date: Thu, 25 Jan 2018 16:10:03 +0300
Subject: [PATCH] fix: Fixes concerning @tbl3rd's review

---
 src/main/java/picard/sam/HitsForInsert.java         | 10 +++++-----
 src/test/java/picard/sam/MergeBamAlignmentTest.java |  4 ++--
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/main/java/picard/sam/HitsForInsert.java b/src/main/java/picard/sam/HitsForInsert.java
index 535193a09d..e18633a1ad 100644
--- a/src/main/java/picard/sam/HitsForInsert.java
+++ b/src/main/java/picard/sam/HitsForInsert.java
@@ -150,7 +150,7 @@ public SAMRecord getSecondOfPair(final int i) {
      * @return the index, or -1 if no primary was found.
      */
     public int getIndexOfEarliestPrimary() {
-        for (int i = 0; i < numHits(); i++) {
+        for (int i = 0; i < numHits(); ++i) {
             final SAMRecord firstAligned = getFirstOfPair(i);
             final SAMRecord secondAligned = getSecondOfPair(i);
             final boolean isPrimaryAlignment = (firstAligned != null && !firstAligned.isSecondaryOrSupplementary()) ||
@@ -247,12 +247,12 @@ void coordinateByMate() {
         final List<SAMRecord> newFirstOfPairOrFragment = new ArrayList<>();
         final List<SAMRecord> newSecondOfPair = new ArrayList<>();
 
-        for (int i = 0; i < firstOfPairOrFragment.size(); i++) {
+        for (int i = 0; i < firstOfPairOrFragment.size(); ++i) {
             final SAMRecord first = firstOfPairOrFragment.get(i);
             newFirstOfPairOrFragment.add(i, first);
             newSecondOfPair.add(null);
 
-            for (int k = 0; k < secondOfPair.size(); k++) {
+            for (int k = 0; k < secondOfPair.size(); ++k) {
                 final SAMRecord second = secondOfPair.get(k);
                 if (arePair(first, second)) {
                     newSecondOfPair.set(i, second);
@@ -262,7 +262,7 @@ void coordinateByMate() {
             }
         }
 
-        for (int i = 0; i < secondOfPair.size(); i++) {
+        for (int i = 0; i < secondOfPair.size(); ++i) {
             if (secondOfPair.get(i) != null) {
                 newFirstOfPairOrFragment.add(i, null);
                 newSecondOfPair.add(i, secondOfPair.get(i));
@@ -278,7 +278,7 @@ void coordinateByMate() {
     }
 
     /**
-     * Identifies weather records present pairwise alignment or not.
+     * Identifies whether records present pairwise alignment or not.
      *
      * It is unnecessary to check QNAME here cause an object of {@code HitsForInsert}
      * presents only records with the same QNAME.
diff --git a/src/test/java/picard/sam/MergeBamAlignmentTest.java b/src/test/java/picard/sam/MergeBamAlignmentTest.java
index 4c00785662..f80efe6589 100644
--- a/src/test/java/picard/sam/MergeBamAlignmentTest.java
+++ b/src/test/java/picard/sam/MergeBamAlignmentTest.java
@@ -1929,7 +1929,7 @@ public void testPairedReadsAreProcessedProperlyInAbsenceOfHitIndexTags () throws
     }
 
     @Test
-    public void testCoordinateByMateMethodWorksProperly () throws IOException {
+    public void testCoordinateByMateMethodWorksProperly () {
         final HitsForInsert hitsForInsert = new HitsForInsert();
         final SAMFileHeader header = new SAMFileHeader();
         header.setSortOrder(SAMFileHeader.SortOrder.queryname);
@@ -1973,7 +1973,7 @@ public void testCoordinateByMateMethodWorksProperly () throws IOException {
             hitsForInsert.addFirstOfPairOrFragment(second);
         }
 
-        for (int i = 0; i < 3; i++) {
+        for (int i = 0; i < hitsForInsert.numHits(); i++) {
             final SAMRecord first = hitsForInsert.getFirstOfPair(i);
             final SAMRecord second = hitsForInsert.getSecondOfPair(i);