Merge pull request #126 from PolinaBevad/f_fix_StringOutOfBound_modifyCigar

Fix for StringOutOfBoundException on modifyCigar

Author: pcingola

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

@@ -460,10 +460,10 @@ public static Tuple.Tuple2<Integer, String> modifyCigar(int indel,
                         if (!ref.containsKey(refoff - rrn - 1)) {
                             break;
                         }
-                        if (isHasAndNotEquals(ref, refoff - rrn - 1, querySeq, rdoff - rrn - 1)) {
+                        if (rrn < rdoff && isHasAndNotEquals(ref, refoff - rrn - 1, querySeq, rdoff - rrn - 1)) {
                             rn = rrn + 1;
                             rmch = 0;
-                        } else if (isHasAndEquals(ref, refoff - rrn - 1, querySeq, rdoff - rrn - 1)) {
+                        } else if (rrn < rdoff && isHasAndEquals(ref, refoff - rrn - 1, querySeq, rdoff - rrn - 1)) {
                             rmch++;
                         }
                         rrn++;
@@ -500,10 +500,10 @@ public static Tuple.Tuple2<Integer, String> modifyCigar(int indel,
                 if (!ref.containsKey(refoff - rrn - 1)) {
                     break;
                 }
-                if (isHasAndNotEquals(ref, refoff - rrn - 1, querySeq, rdoff - rrn - 1)) {
+                if (rrn < rdoff && isHasAndNotEquals(ref, refoff - rrn - 1, querySeq, rdoff - rrn - 1)) {
                     rn = rrn + 1;
                     rmch = 0;
-                } else if (isHasAndEquals(ref, refoff - rrn - 1, querySeq, rdoff - rrn - 1)) {
+                } else if (rrn < rdoff && isHasAndEquals(ref, refoff - rrn - 1, querySeq, rdoff - rrn - 1)) {
                     rmch++;
                 }
                 rrn++;

src/test/resources/com/astrazeneca/vardict/integrationtests/172N_S7.final.chr1_sliced_SOOBE.bam

@@ -0,0 +1,2 @@
+Somatic,hs38DH.fa,172T_S8.final.chr1_sliced_SOOBE.bam|172N_S7.final.chr1_sliced_SOOBE.bam,chr1,11182030,11182188
+172T_S8.final.chr1_sliced_SOOBE	testbed	1	11182181	11182181	A	G	359	5	132	221	2	3	A/G	0.0139	2;2	32.8	1	37.8	1	60.0	10.000	0.0144	0	1.2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1.000	1	GGATGACAGCGTATCTCTGG	TGCTGGCGCCCACAGAAAAG	1:11182031-11182188	SampleSpecific	SNV	0	0	0	0