From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 21 Mar 2018 17:45:17 +0000 (+0000)
Subject: JAL-2909 update tests for stranded insert map and writeback of mapped read extent... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Fspikes%2Fkira;hp=14ff5041c38ee2df9c2055ba2c7bd51b548bbe04;p=jalview.git

JAL-2909 update tests for stranded insert map and writeback of mapped read extent via Range
---

diff --git a/test/jalview/datamodel/CigarParserTest.java b/test/jalview/datamodel/CigarParserTest.java
index 80121ee..476721c 100644
--- a/test/jalview/datamodel/CigarParserTest.java
+++ b/test/jalview/datamodel/CigarParserTest.java
@@ -101,7 +101,7 @@ public class CigarParserTest
     rec.setAlignmentStart(start);
 
     CigarParser cp = new CigarParser('-');
-    String bfresult = cp.parseCigarToSequence(rec, insertions, 1);
+    String bfresult = cp.parseCigarToSequence(rec, insertions, 1, null);
 
     System.out.println(result);
     System.out.println(bfresult);
@@ -128,7 +128,11 @@ public class CigarParserTest
 
     Iterator<SAMRecord> it = builder.iterator();
     CigarParser cp = new CigarParser('-');
-    SortedMap<Integer, Integer> insertions = cp.getInsertions(it);
+    Range xtent[] = new Range[] { new Range(0, 0) };
+    SortedMap<Integer, Integer> insertions,
+            insertStrands[] = cp.getInsertions(it, xtent);
+    Assert.assertEquals(insertStrands.length, 2);
+    insertions = insertStrands[0];
     Assert.assertEquals(insertions.size(), 6);
     Assert.assertTrue(insertions.containsKey(28838));
     Assert.assertEquals((int) insertions.get(28838), 1);