Merge pull request #293 from PolinaBevad/issue_283_hardclips

Fix issue 283 hardclips Index out of range error

Author: pcingola

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

@@ -880,6 +880,10 @@ private boolean isInsertionOrDeletionWithNextMatched(int ci) {
 
     private boolean isCloserThenVextAndGoodBase(String querySequence, Map<Integer, Character> ref, String queryQuality,
                                                 int ci, int i, StringBuilder ss, CigarOperator cigarOperator) {
+        // Do not adjust complex if we have hard-clips after insertion/deletion
+        if (cigar.numCigarElements() > ci + 2 && cigar.getCigarElement(ci + 2).getOperator() == CigarOperator.H) {
+            return false;
+        }
         return instance().conf.performLocalRealignment && cigarElementLength - i <= instance().conf.vext
                 && cigar.numCigarElements() > ci + 1
                 && cigar.getCigarElement(ci + 1).getOperator() == cigarOperator

src/test/resources/com/astrazeneca/vardict/integrationtests/test_reads.hardclipped.bam

@@ -1,2 +1,3 @@
 test,5234,7764,NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAATATTTCCACTTGCATATGCAGGTACACACACAAAAGGGATAAATGTGGGGTTTTTTTTTCACTTTAAAGTAACTACAACCCTTATTTCAGAGTCATTATATAACTAAATTCTTTAAATATCTATTATTCTAGGATTGAAATCACTCTTTACAGGACTTCAGTGCATGTTTTTGATTGGAAATTACTTTCAAAAGAGATCTACACATATGCACACATGCACACAACTACACATATTGCACCACAGCTACCTACTCTTCTAAAGCTGAGGAAATGTTCACTTTGGGGGGAGGAGTTGTTTTGTTTTGTTTTGTTTTGACCAGGGTCTCAGCATGCCAGGCTGGCTGACCTGGAGCTCACAGAACCCTCTGAACATCTGCCTCCCAGTGGTAAGATTAAAGGAATGCACTGCCATGTACAGCGCACCCTTTCTTTTCTGAGAAGTATTTTTCGATCTTGTCCGCCCTCCGTATTCATTCAGTATACAGGCAACTACGGTCCACCTCCACTGAAAACAAAAGGTCACTGCACCACTTTTACTCAGGCTTGAGAGAGCAGAAAGTCCACGGCAGCTATAATCCATTCATTGTGTGCGTCTGCCTGTGCCTGTGCCCCAGTGAGTGGCTCGAGGAGACACAAGGACAGCATGTGGGAGCCCATTCCTCCCATCCCAACTCACCATTCCATGGTGGGGTCCTTCCCTCACTACTGTACACCCCAGTTGCATGCCAATGCCCAAGCCAAGCTCCCCTGGGTGCTGTGCTCAAGCCCGAGACTGTATTAACGAAAGCTCCTGTTCACCGGGTATAACCACGGTTTACACAGCTTTAATCCTAGCACTGAAGGCAGAAGCAGGCACATCTTCGTGAGTTTGGAAGCCAGCCTCGTTCACCTAATGAGTTCCAGGGCAGACACAACTACATTAGTAATACCTGTCTTTAAAAAAAAAAAAAAAAGATTGTTACAATGAACCACTGTAACATGAAATCGCCAAATGCAAAAGCTTTAGTACACAGTTAATAAATGTGAAGTTGTCCTGTGCCCTCCCCATTACCTGTGGCAACGCGTCTCTTTTTCCCCCTCCACACAAAATAAATGAAAATTTAAAAGACAGATTTTTTTTTTTAGGATTTTATTTGTTCAAAATAAAATCCAGTGTCTAACCCTTGGACTCCCACTGGAGCTGCAGGGAGCCGGCCCGCCCTGCCCCTCCTCCACACTAGGGCTCTCCCACTCTCTCCCATCCTTAATCTCTAAGAGGCCCCTTCAAAGCCAGGCCAGTGGGGATTTTGCTAAACTACCAGATTATGCCTCTGCCTTTACAGTCTCTCTATTGCTCCTAAATCTACAAAAGCAAACCTTCAATAGGACCTTGCTTTTCCCACTCCCTCAAGAGCCCCAGGCTGGCTCAGAGCCACCTACCCATCAGCTCACCAGGACAACCTCCACCCTCACGGTCACTGACCACTGAGCAGACAGACAGCAAGCCTCTCCTGCCACTCAAGGCCTATAAGTGCCTTAAAAACTGTCATTACCCGGTTGTTTACTCTCATGTCAGAGGAAACCAATCTCGCTGTCTACTGAAAGCACACACTGACTTAAATGCACCCACAGCAGCAGGGTCAAACACAAGTGATCATCATGCAGAAACTACCGTGGAAAATGTGCAGAACCTGAAGGACGGTGGCTCACAGGGCTCAAGAAGTCAGATTTGCCTGTGAAAGAGAGCAGTCCTAGAAAGACTCTTAAACACATATTCAATCCAATACCATTTAACACACCGCTTTTCTTCAATCCATTCTCTTAATAGTTTCTCTATCGTCTTGGATTATCTCCCATTCTCATTTCATGTGCCATCTGCTCGTTTAAGACTTCACGTCTGTCCAGTCTCTGAAATATTTGTCACTTTAGTCATTAGCACCTTGCACAATGCAGCTCTGTCTCCTTAAAGTTCAGAGCTCGATTATTTTAGAAAGCTCAAGATTATTTTAACATCACCATTTCTTAATCTAAACTGGCCTGCCTACACTTTACATTTTCCACCTAATGAAAATTCCACCTCAGTAAGTGTCCGTGCTGTTTTAAAAGGAAGCCGAGAAGCAGGGCCATAAACTAGAGGGTTCTACAGGCCACCTCAGCAAATTCTCCCAAGCAAACTCAAGAGCTGTGACAGAGTCCCACAGAACTCCCTTCTCACTCCCCAGCAGGCCCCAGCCTACTCTCTACCCCTCCCAGGGCCAGCAGAAAGTTCCCCTCTGGTCTTCTCAGTTTCAAGGCATCACGCAGCCCATGCAGCTCCCTCTGGGCCTGACATACAGCATCTCAGAAATTAAATCGTACGTGTA
-test,5475,8024,CACCAGCTCACCCTCCCTGGGCCGTGGCCACTCTGGCTTTGGCTCAGCCCAGCCTGGAGTTCGGCTATTTCAGAGAGGGAAGCCAGAGGAGAAGAGGGTGCAGGCTGAGGTCCCCACAAATCTGCCCCCAGAGCCCTGGCAAGTGGACCCGCCAATCCCGAGGAAGAACCGGAGGACTTGGGACAGCTCAGACCACCAAGTCTCCAAGTCCTTGTTAGAAACAAGAGCAAAATAAATTATTTTTGCCTAATCCTTTTTCCTTCTAAAAATGGTTGCCTTCGTCTGTCCCGTCCCCTCCTTTTCTCTACATAAAGTTGTCCTTGTTGTTCTCCAAACAACTGTCCATGCAGGAAACCCCACCTGGGCAGCGGTCAGGTGCGGAGGCAGCCTCTCAGCGGTGGGGAACATTCACAGTAACTGCTGGCAGGCTGCTGGGCGCCCTCCAGGAGAGGGGGTGCTGGGCCGAGCCGGGCTGGCAGGAGTGGTGTCGGCCTTCGGGAAATGCTGGGCTGCTAAGGGTTTGGTCCACCCATCCCGGGAGTGCCCGGTCCTCGACGTCCATCTGTTCCCTAGCCCATGGCGGTCACCATGCTGGACGGGTGGGGGTGGCCGAAGGAGAGGCTGGAGGAGGGGTGGATGGGCGTCGGAGTGGGCAGGATGTGTCCGGAGTGGCTGAAGGGCGGGAGGTGGCCCACAGGTGCCATGTGTCCAGCCAGGGCAGCTGCACTGAAGGGGGATGACTTCTCCTGCATGCACTTTGACAGCTCCTCGAAGCACTCCGCCCCTTTCTTGCTCTTCTTGGACTTGTTGGACATCTTCCGGTTCCGAGTCTGGATCCCTTCCTTCTTCATGGTCAGTGGCCTGTTAACCTAGAGGCAACCACCAGTTTTCAGAGGGCCAGTTCCTTCCTCCAGCAACATTCCTCCCACCCCGCCACAGCGTGGACCAGAGGCAGGTCAAGCTGAGGGTCCCAGGAAGCCAGGAATTGTGCCCGACCTTCATAGTCCCATCACCAGATGGCTACCATTCCAGGAAGGGCGGGTTCTGGCATATGGGGCTGACCCACACCCTCCCTGGCTCTGCCCACCGCATGCCAGCACTGCCCAGCCAACTGAAGTCCTCCCCCCCACCCTGACCCTTTTTAAGCAGAGAAACCACTTCCCTAGTCCGAGACCCTGTCCTAGCCAGCTCCACCTCCTGAGCAGAGGCAAGGCACCCCTCTTACGGGAAGCCCTTCTGGCGCTCACTCAGGGCAGCAGCTTCCCAAGCCAAGCCAAGCTGGATATTGTGGCTGGGGCCTCTTGCCTGGCAGCACAAAGCGCAGAGGTCCCCTGGGAGGGGCGGGGTGGCCGGGGCGGGGCGCACTCACATTGTGCAGCTTGTAGTAGAGGCCACAGGCGTTGCAGACAGGGTCCCCGTTGGCGTTTCGGCGCCATAAGGTGGTGGTTGTCGTCTGACAATTTGCACAACAGGTGCCGGCTCTTCTGGCGGCCGACTGGGAGGGCAAGGCAGCGTCAGCAGGCTGGACTCCCACGCCCACCTCGACCCCCCTCCCTGACCCTCGCTCCACCCCCAGTCCCCACCAGCTCAGTCAAGGAGGGCTAAATCTCACATGGGAATCAAAGCATCTCAGAACCATGGAATTTTAGAATTTGAGAACGAAATAAGTCAAGACTCACAGAACTTTGGAATAAAGAACTCTCAGAAGCCTGATGTTAGAATCAACGGGATTGCAAGAGCTACAGAGGAGAATTAGCTACCTCCCCCAACTACCCTGCGCTCTAACTCCATAAATGGGGAAACTGAGGCCCTGAGAAGGGCTCTCTAGTAGCACAGGCATCCTGAGGCTGAGCCGGCTTGGTCCCCCTCGAGCCCCTGGATCTGGGGCCGATTCTGTGTCTCCTCTAGCACGACTCCGCTCAAAATCCATAATCCTGGGTGAGTCAGTGTCGCTGAGGCCAGCGCAGGTTTACAGAGTGCAGAGCTGCACCGTCCAACACTGTAGCAGCTGGCCACAGGCAGCCATTTAAATAAGATCTAACTACAAATTAACAAAATTAAAAACCCAGTTCCCTCAATTGCACGAGCCACATTTCAAGTGATCAATATTCACATGTGGCCAGGGGCTACCACAGTGGGCAGTGCAGACACAGAACTTTTCCATCTCTCCAGCTGATGTGAGTGCTGATCCCCCCCATCCAGCCCCCCATACCCCAACCCTTAGAGCTTTAACCACCCCGCAGCCCCTCTGAGTCCTAGTCCCTCAGGAAATGCCTGGCAGAGGTAGGGTCTGGAAATGAGCGCCTGGTCCTTGCAGAGAGAAGCTAGAGGGAGGCTTTACCCAAGAAAACAGATCCCCTCTCCCGGTTCCACCAACGCCAGCCCCACAGTGACAGAGGGGGTCCCCCAACACTTCCCAGAGAACTGCAGGCGGGAGTGCACCAGGTGGTGAGTGTGGGGGGCTGGGGGCTGAGGCCTGCAGAGCCTGGAACAGCCCCAGGCCCAAGCCTGGTCACAGAAGGGACAGAGGGACTGCAGCCGCGGGGGCAG
+test,5475,8024,CACCAGCTCACCCTCCCTGGGCCGTGGCCACTCTGGCTTTGGCTCAGCCCAGCCTGGAGTTCGGCTATTTCAGAGAGGGAAGCCAGAGGAGAAGAGGGTGCAGGCTGAGGTCCCCACAAATCTGCCCCCAGAGCCCTGGCAAGTGGACCCGCCAATCCCGAGGAAGAACCGGAGGACTTGGGACAGCTCAGACCACCAAGTCTCCAAGTCCTTGTTAGAAACAAGAGCAAAATAAATTATTTTTGCCTAATCCTTTTTCCTTCTAAAAATGGTTGCCTTCGTCTGTCCCGTCCCCTCCTTTTCTCTACATAAAGTTGTCCTTGTTGTTCTCCAAACAACTGTCCATGCAGGAAACCCCACCTGGGCAGCGGTCAGGTGCGGAGGCAGCCTCTCAGCGGTGGGGAACATTCACAGTAACTGCTGGCAGGCTGCTGGGCGCCCTCCAGGAGAGGGGGTGCTGGGCCGAGCCGGGCTGGCAGGAGTGGTGTCGGCCTTCGGGAAATGCTGGGCTGCTAAGGGTTTGGTCCACCCATCCCGGGAGTGCCCGGTCCTCGACGTCCATCTGTTCCCTAGCCCATGGCGGTCACCATGCTGGACGGGTGGGGGTGGCCGAAGGAGAGGCTGGAGGAGGGGTGGATGGGCGTCGGAGTGGGCAGGATGTGTCCGGAGTGGCTGAAGGGCGGGAGGTGGCCCACAGGTGCCATGTGTCCAGCCAGGGCAGCTGCACTGAAGGGGGATGACTTCTCCTGCATGCACTTTGACAGCTCCTCGAAGCACTCCGCCCCTTTCTTGCTCTTCTTGGACTTGTTGGACATCTTCCGGTTCCGAGTCTGGATCCCTTCCTTCTTCATGGTCAGTGGCCTGTTAACCTAGAGGCAACCACCAGTTTTCAGAGGGCCAGTTCCTTCCTCCAGCAACATTCCTCCCACCCCGCCACAGCGTGGACCAGAGGCAGGTCAAGCTGAGGGTCCCAGGAAGCCAGGAATTGTGCCCGACCTTCATAGTCCCATCACCAGATGGCTACCATTCCAGGAAGGGCGGGTTCTGGCATATGGGGCTGACCCACACCCTCCCTGGCTCTGCCCACCGCATGCCAGCACTGCCCAGCCAACTGAAGTCCTCCCCCCCACCCTGACCCTTTTTAAGCAGAGAAACCACTTCCCTAGTCCGAGACCCTGTCCTAGCCAGCTCCACCTCCTGAGCAGAGGCAAGGCACCCCTCTTACGGGAAGCCCTTCTGGCGCTCACTCAGGGCAGCAGCTTCCCAAGCCAAGCCAAGCTGGATATTGTGGCTGGGGCCTCTTGCCTGGCAGCACAAAGCGCAGAGGTCCCCTGGGAGGGGCGGGGTGGCCGGGGCGGGGCGCACTCACATTGTGCAGCTTGTAGTAGAGGCCACAGGCGTTGCAGACAGGGTCCCCGTTGGCGTTTCGGCGCCATAAGGTGGTGGTTGTCGTCTGACAATTTGCACAACAGGTGCCGGCTCTTCTGGCGGCCGACTGGGAGGGCAAGGCAGCGTCAGCAGGCTGGACTCCCACGCCCACCTCGACCCCCCTCCCTGACCCTCGCTCCACCCCCAGTCCCCACCAGCTCAGTCAAGGAGGGCTAAATCTCACATGGGAATCAAAGCATCTCAGAACCATGGAATTTTAGAATTTGAGAACGAAATAAGTCAAGACTCACAGAACTTTGGAATAAAGAACTCTCAGAAGCCTGATGTTAGAATCAACGGGATTGCAAGAGCTACAGAGGAGAATTAGCTACCTCCCCCAACTACCCTGCGCTCTAACTCCATAAATGGGGAAACTGAGGCCCTGAGAAGGGCTCTCTAGTAGCACAGGCATCCTGAGGCTGAGCCGGCTTGGTCCCCCTCGAGCCCCTGGATCTGGGGCCGATTCTGTGTCTCCTCTAGCACGACTCCGCTCAAAATCCATAATCCTGGGTGAGTCAGTGTCGCTGAGGCCAGCGCAGGTTTACAGAGTGCAGAGCTGCACCGTCCAACACTGTAGCAGCTGGCCACAGGCAGCCATTTAAATAAGATCTAACTACAAATTAACAAAATTAAAAACCCAGTTCCCTCAATTGCACGAGCCACATTTCAAGTGATCAATATTCACATGTGGCCAGGGGCTACCACAGTGGGCAGTGCAGACACAGAACTTTTCCATCTCTCCAGCTGATGTGAGTGCTGATCCCCCCCATCCAGCCCCCCATACCCCAACCCTTAGAGCTTTAACCACCCCGCAGCCCCTCTGAGTCCTAGTCCCTCAGGAAATGCCTGGCAGAGGTAGGGTCTGGAAATGAGCGCCTGGTCCTTGCAGAGAGAAGCTAGAGGGAGGCTTTACCCAAGAAAACAGATCCCCTCTCCCGGTTCCACCAACGCCAGCCCCACAGTGACAGAGGGGGTCCCCCAACACTTCCCAGAGAACTGCAGGCGGGAGTGCACCAGGTGGTGAGTGTGGGGGGCTGGGGGCTGAGGCCTGCAGAGCCTGGAACAGCCCCAGGCCCAAGCCTGGTCACAGAAGGGACAGAGGGACTGCAGCCGCGGGGGCAG
+example_genome,1,540,TCTGCTGTGTCACCTCAACGATGCGTGTATCAGTAACCCCTGCAACGAGGGCTCCAACTGCGACACCAACCCTGTCAACGGCAAGGCCATCTGCACCTGCCCCTCGGGGTACACGGGCCCGGCCTGCAGCCAGGACGTGGACGAGTGCTCGCTGGGTAGGTGCTGGCACAGGGGGTGCGTCCGGATGGGGGTAGCAGCCTGGCCCCAGAGCCGGTGGGAAGTCATTTCTGGCTTCAGGGGGTGCTCAGTTGGATGGGGTATGGGACCCTGCCAGTCCGACGTGGGGGATGTGCGGCGAGGTGTTGCAGGGGCCAGAGTGCCTGGAGAAGCCTCTCACCCGTGTGCCCTTGCCAGGTGCCAACCCCTGCGAGCATGCGGGCAAGTGCATCAACACGCTGGGCTCCTTCGAGTGCCAGTGCCTGCAGGGCTACACGGGCCCCCGCTGCGAGATCGACGTCAACGAGTGTGTCTCGAACCCGTGCCAGAACGACGCCACCTGCCTGGACCAGATCGGGGAGTTCCAGTGCATCTGCATGCCTG

src/test/resources/com/astrazeneca/vardict/integrationtests/test_reads.hardclipped.bam.bai

@@ -0,0 +1,7 @@
+Simple,hard_clip_case.fa,test_reads.hardclipped.bam,example_genome,160,280,-f 0.0 -P 0
+test_reads.hardclipped	testbed	example_genome	224	224	A	G	4	4	0	0	0	4	G/G	1.0000	0;0	38.8	1	41.0	0	60.0	8.000	1.0000	0	0	3.000	1	3.0	4	4	CCCAGAGCCGGTGGGAAGTC	TTTCTGGCTTCAGGGGGTGC	example_genome:161-280	SNV	0	0
+test_reads.hardclipped	testbed	example_genome	259	259	T	G	4	4	0	0	0	4	G/G	1.0000	0;0	29.0	1	41.0	0	60.0	8.000	1.0000	0	3	1.000	1	3.0	4	4	GGGTGCTCAGTTGGATGGGG	ATGGGACCCTGCCAGTCCGA	example_genome:161-280	SNV	0	0
+test_reads.hardclipped	testbed	example_genome	278	278	G	A	4	4	0	0	0	4	A/A	1.0000	0;0	10.0	1	41.0	0	60.0	8.000	1.0000	0	0	1.000	1	3.0	4	4	GTATGGGACCCTGCCAGTCC	ACGTGGGGGATGTGCGGCGA	example_genome:161-280	SNV	0	0
+test_reads.hardclipped	testbed	example_genome	185	185	A	G	4	4	0	0	4	0	G/G	1.0000	0;0	3.0	0	41.0	0	60.0	8.000	1.0000	0	2	1.000	1	1.0	4	4	GGCACAGGGGGTGCGTCCGG	TGGGGGTAGCAGCCTGGCCC	example_genome:161-280	SNV	0	0
+test_reads.hardclipped	testbed	example_genome	186	186	T	TG	7	7	0	3	4	3	T/+1	1.0000	0;2	1.0	0	41.0	0	60.0	14.000	1.0000	0	5	6.000	1	1.9	7	7	GCACAGGGGGTGCGTCCGGA	GGGGGTAGCAGCCTGGCCCC	example_genome:161-280	Insertion	0	0
+