git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2909 update tests for stranded insert map and writeback of mapped read extent...
[jalview.git]
/
test
/
jalview
/
datamodel
/
CigarParserTest.java
diff --git
a/test/jalview/datamodel/CigarParserTest.java
b/test/jalview/datamodel/CigarParserTest.java
index
80121ee
..
476721c
100644
(file)
--- 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('-');
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);
System.out.println(result);
System.out.println(bfresult);
@@
-128,7
+128,11
@@
public class CigarParserTest
Iterator<SAMRecord> it = builder.iterator();
CigarParser cp = new CigarParser('-');
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);
Assert.assertEquals(insertions.size(), 6);
Assert.assertTrue(insertions.containsKey(28838));
Assert.assertEquals((int) insertions.get(28838), 1);