Fixes StringOutOfBoundException for cases of three indels/three deletions/ two deletions and insertion

Added test case

Author: PolinaBevad

src/main/java/com/astrazeneca/vardict/VarDict.java

@@ -524,6 +524,9 @@ static int somdict(Region segs, Map<Integer, Vars> vars1, Map<Integer, Vars> var
         Collections.sort(pp);
 
         for (Integer p : pp) {
+            if (p < segs.start || p > segs.end) {
+                continue;
+            }
             Vars v1 = vars1.get(p);
             Vars v2 = vars2.get(p);
             if (v1 == null && v2 == null) { // both samples have no coverage

src/main/java/com/astrazeneca/vardict/modules/CigarUtils.java

@@ -194,7 +194,7 @@ public static Tuple.Tuple2<Integer, String> modifyCigar(int indel,
 
                 //number of bases after refoff/rdoff that match in reference and read
                 int rn = 0;
-                while (isHasAndEquals(querySeq.charAt(rdoff + rn), ref, refoff + rn)) {
+                while (rdoff + rn < querySeq.length() && isHasAndEquals(querySeq.charAt(rdoff + rn), ref, refoff + rn)) {
                     rn++;
                 }
                 RDOFF += rn;
@@ -247,7 +247,7 @@ public static Tuple.Tuple2<Integer, String> modifyCigar(int indel,
 
                 //number of bases after refoff/rdoff that match in reference and read
                 int rn = 0;
-                while (isHasAndEquals(querySeq.charAt(rdoff + rn), ref, refoff + rn)) {
+                while (rdoff + rn < querySeq.length() && isHasAndEquals(querySeq.charAt(rdoff + rn), ref, refoff + rn)) {
                     rn++;
                 }
                 RDOFF += rn;
@@ -301,7 +301,7 @@ public static Tuple.Tuple2<Integer, String> modifyCigar(int indel,
                 }
 
                 int rn = 0;
-                while (isHasAndEquals(querySeq.charAt(rdoff + rn), ref, refoff + rn)) {
+                while (rdoff + rn < querySeq.length() && isHasAndEquals(querySeq.charAt(rdoff + rn), ref, refoff + rn)) {
                     rn++;
                 }
                 RDOFF += rn;

src/test/resources/com/astrazeneca/vardict/integrationtests/N13532.TwoDels1InsStringBoundError.bam

@@ -0,0 +1 @@
+11,1278939,1281541,CGGTAAGACGCTGCAGAGCAGAGGTGCCCGGCATAGGGTGAGGGGGGACAGAGCCGGTGCCCACCAGGGGCCTGTGGGTTGGGCACAGGAGAGCAGAGGAGAGCCACTGTGTCCTGGCGTGACCGCGGCAGGACCACTCGGCAGAGATGGCCTCCAGGTGCTTCATTCTCCTCCTAACGATGAGGCTGGTGACCTCTGGCCTGCCCAGGAGTGGCCCAGGGACGTGGGAAGCAGCGGGGAGGTGGCCAAGCAAGGGGCCTGGAGGGAGCCCCCAGGGGCTGTGAAGCGGTCAGGTCCTCGGGGAAAAGCACGCCTGCGACTTACTCTGGGAACAAGTGGTCGGGAGGAGGAGTGAGCAGCGCCCAGACAGTGGCCTCCATCCTCCCGCAGTGTGCAACACAACCACCTGCCCCCAGAGCCTGCCTGTGTGCCCGCCAGGGCAGGAGTCCATCTGCACCCAGGAGGAGGGCGACTGCTGTCCCACCTTCCGCTGCAGTGAGCGGGGCTGGGGCCGGGCTCCTGGGTGGCCTCTTGCTGGGGGTGGGGGAGTGCAGGATGGTGGGGGCGCTGGAGCACATGCTCCCCACCACTTGTCGAGGGCTTAGCTCCCTTTCCTTCCAGGACCTCAGCTGTGTTCGTACAATGGCACCTTCTACGGGGTAAGGGCACAGCAGTGGGTGGGTGTGGCCCTGGGGCCTGAACATGTGTGTGGGATGCCCCGGGGCTCTCTGAGCCCCACTCCTTGTCTTGACATTCCTGCCCTGAGGGCCGATCCGCACAGGGGCCCTGGACACGTCAGAGCTGGGACATGCTTGGGACTCAGGGGCACCTTACGTCGACAGCCATGAGCTCCACAACTGCTGCCTCTGAGAGGTCCCTTCAGGGGCTCCCAGCAACAGCCTGGGGGCAGCACACACTGGCCTGGGGTCCCCGCCTGCCCGCCCAGATTCCTACCCGCCCGGATTCCTGCCTGCCAGATTCCTGCCCCCATGGGGTCTCTGCCCACCCAGATTCCTGCCCACATGGGGTCTCTGCCTGCCCAGATTCCCTGCCCACCTGTGGTCCCTGTGTGCATCAGCTCCCTGCCTGCCTGGGTCCATGCTCAGCCAGGGGTGCATCTATGCTCCATCTGAGGAAGGAACAACTCCCTGCAGGCCCCATTGGGTCATGGGGAGGGGTCCTGGCCCTGTTGCCCCACCAGTGCCCTCAGTGCCACCCTCCCACCCCTTGCAGGTTGGTGCAACCTTCCCAGGCGCCCTTCCCTGCCACATGTGTACCTGCCTCTCTGGGGACACCCAGGACCCAACGGTGCAATGTCAGGAGGATGCCTGCAACAATACTACCTGTCCCCAGGTGAGACCCGAGGCACCTGCCCCCAGGTGAGCCCCCGAGGCACCTGCCCCCAAGTGAGACCCGAGGCACCTGCCCCCAGGTGAGACCTGAGTCACCCGCCCCCAGGTGAGCCCCCGAGGCACCTGCCCCCAGGTGAGTCCCTGAGGCACTTGCCCCCAAGTGAGACCCGAGGCACCTGCCCCCAGGTGAGACCCGAGGCACCTGCCCCCAGGTGAGACCTGAGTCACCTGCCCCCAGGTGAGCCACCAAGGCACCTGCCCCCAAGTGAGACCCGAGGCACCTGCCCCCAGGTGAGCCCACAGCTGCTGGGCAGACCCAGCCCTGAGTCACTTATCCTGGCTCCCTGGGGTTCTCTAGCTCAGCCATTGCTGGGGTCTTGTTTGTTTCCAAAGGGAGGGTATGAAGTAGGAGGATAACTGAGGGGGTCTGGGGGTGGGACAGGACCTGCAGGCTGCTGGGGACAGGGGCTGAGGTCAGGTTCCAGGAAGGCAGGGGTAGGCAGAGAGAAGGTGCTGGAAACTGGGGTGAGGCTGAGCCGGGATAACTGAGTGGGGGCAACTTCTTCGGGTATAGGCCCAGGCAGGGACAGGGCTAAGGGGTCCTGGACCACTGGGGTGTAGACAGGAGGGCAGGCTGGGCCGGGGCATGTGCTGGAGGAGAGGGTTAGGGCCTGACGCCCCTCATGTCCCCACAGGGCTTTGAGTACAAGAGAGTGGCCGGGCAGTGCTGTGGGGAGTGCGTCCAGACCGCCTGCCTCACGCCCGATGGCCAGCCAGTCCAGGTAACAGCAGAGGCATGTGGGGGCAGGTCTCAGCTCCCTCCCTGGAGACCCTCACCCCCAATGGGGCTCTGCACAAGAGGTAATCCCTACTCAGCTTCCACACTCACCCTTGCATTTCAGCTGAATGAAACCTGGGTCAACAGCCATGTGGACAACTGCACCGTGTACCTCTGTGAGGCTGAGGGTGGAGTCCATTTGCTGACCCCACAGCCTGCATCCTGCCCAGATGTGTCCAGCTGCAGGGTGTGTGCTGGAGGCCCTGCCCCTGCCTGGGAGTCCTTGTCCATCAGGGAGGCCCAACCCCTGTCTGGGATGCCCTGCACAGCAGGGAGGCCCCACCCCTGCTGGGGAGGCCCCACCCCTGCCTGGGAAGCCCCACCCCTGCCTGGGAGGCCCCGCCCCTGCCCGGGAGGCCATGCCCCTGCCCGGGTGGGCCCCTCCCCAGGAGGCCGCACCCACCAGGGAGGCC

src/test/resources/com/astrazeneca/vardict/integrationtests/N13532.TwoDels1InsStringBoundError.bam.bai

@@ -0,0 +1,3 @@
+Simple,GRCh37.fa,N13532.TwoDels1InsStringBoundError.bam,chr11,1280138,1280341,-f 0.0025 -F 0x700 -Q 10
+N13532.TwoDels1InsStringBoundError	testbed	11	1280291	1280344	GGTGAGACCCGAGGCACCTGCCCCCAGGTGAGCCCCCGAGGCACCTGCCCCCAA	G	3733	39	1693	1990	0	39	G/-53	0.0104	2;1	48.6	1	34.3	1	48.5	78.000	0.0112	0	31	2.000	1	3.6	39	3488	AACAATACTACCTGTCCCCA	GTGAGACCCGAGGCACCTGC	11:1280139-1280341	Deletion	0	0
+N13532.TwoDels1InsStringBoundError	testbed	11	1280301	1280301	G	A	3708	33	1606	2012	11	22	G/A	0.0089	2;2	49.1	1	37.1	1	58.1	10.000	0.0088	0	0	1.000	1	1.8	30	3409	CCTGTCCCCAGGTGAGACCC	AGGCACCTGCCCCCAGGTGA	11:1280139-1280341	SNV	0	0