From 70f98ab214fefd664892e8c8ec44811d820a802d Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 21 Mar 2018 17:45:17 +0000 Subject: [PATCH 1/1] JAL-2909 update tests for stranded insert map and writeback of mapped read extent via Range --- test/jalview/datamodel/CigarParserTest.java | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) 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 it = builder.iterator(); CigarParser cp = new CigarParser('-'); - SortedMap insertions = cp.getInsertions(it); + Range xtent[] = new Range[] { new Range(0, 0) }; + SortedMap 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); -- 1.7.10.2