Merge pull request #121 from PolinaBevad/f_fix_insertion_end

Fixed issue with coordinate end for insertions

Author: pcingola

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

@@ -3410,13 +3410,7 @@ public int compare(Variant o1, Variant o2) {
                     vref.msint = msint.length();
                     vref.shift3 = shift3;
                     vref.sp = sp;
-                    // In perl it was changed to simple ep
-                    final Matcher pnMtch = PLUS_NUMBER.matcher(genotype);
-                    if (pnMtch.find()) {
-                        vref.ep = sp + toInt(pnMtch.group(1));
-                    } else {
-                        vref.ep = ep;
-                    }
+                    vref.ep = ep;
                     vref.refallele = refallele;
                     vref.varallele = varallele;
                     vref.genotype = genotype;
@@ -4578,7 +4572,6 @@ private static List<Object[]> fillTmp(Map<Integer, Map<String, Integer>> changes
     private static final Pattern BEGIN_MINUS_NUMBER_ANY = Pattern.compile("^-\\d+(.*)");
     private static final Pattern UP_NUMBER_END = Pattern.compile("\\^(\\d+)$");
     private static final Pattern ATGSs_AMP_ATGSs_END = Pattern.compile("(\\+[ATGC]+)&[ATGC]+$");
-    private static final Pattern PLUS_NUMBER = Pattern.compile("\\+(\\d+)");
     private static final Pattern SA_CIGAR_D_S_5clip = Pattern.compile("^\\d\\d+S");
     private static final Pattern SA_CIGAR_D_S_3clip = Pattern.compile("\\d\\dS$");
 

src/test/resources/com/astrazeneca/vardict/integrationtests/NA12878.chr6_137219200-137219700.bam

@@ -0,0 +1 @@
+chr6,137218001,137220900,AGTCTGTGCCTAAGTGCAAGCTCTTACCGCAAAGTACTGCAACTGCCCATGTGGATGACTGACTAGAGCCtagaagagcagttaagaacttggactctggagccaaattgagcagctccccactgagtggctatgacctctctgccagttgggcaggcctctccgtaactcaatttctcgtccataaagagagagacaaataacgcctactccagaagattgttgtgaACACAGAACCAAAACGTGGACCTTTCAAAGTCCCTATGAATCATAAATCATAATAAAAAAAAGAAAACTGAATTGAAAAGGTTTACTGTTTTCTCTGGAGCTCGTAATCACAATTACTCTGCACTTCAGAAAAGCCACCCTCAACATTTGTTTTCTAGGAAATGTCAATAAGCAGGTGGAAATAAAATGCTCCGAAGAACAAACCCGTACGAAGAGACCTACTGCCAAATCTGCTAGTGAGTGCCGGCAATCCACCACTTCCAGACTGAGACCTAAGACGGACTGCCACTTACTTCTCAGCTGCCACTTACTTCTCAGCTGGCGACATAATGCATACTTTCCTACCCTAAGCACTTTGAGTCCCCCCCCCCACCCCCGCTAAGAAAGAAGTATTTAAGCCACGAACTGAGACCACGATGCCACATGCTGATCAGGACACTCAcagtcatgcgtcacttaacgatggagatccgttctgagaaatggagaaatgtccccttaggcaatttcttcgggcagtagaaacccagacaaacccagatgacacagcctactgctcttaggtcatgaacctgtacagcctgtcactgcactgaacactgcaggcaaccgtagcatactagtgagtatctgcgtatctaaccataaaaaaaggtacagtaagaagacgatattataatctttgagaccacgctgtcccacattgaccagcaacgtccttctgcagcgcataaTCGTATTTAAAAGTGGATTACAAGAGTCGGAAAAACAAGCGGCGTGATTTGTTGTGGCGGCAACCAGGGAAGAGGCAGGAGAAAGGCAACCGACGAGTTCAAACCACGGAGCCCCAGTCTCGCGACCCCACCTCGCGTCCCCGTCGCCCGCTCAGGGCCCGACGCAGGGGTCCCGGGCTAGGGCGACCTCGGAGAAGCGGGGCGGGGCTTCCCGGCTGGGGCGGATCCCTCCCTCCCTCTCGTCCCGACCCGGCCGCAGCCCTGCCGCGAACGACGGTACCTGAGGACGGCCCCAGATCCGCGGTGCCCATCTCAGCCCTGCTCACACCCTGCATGACAAGGGGTAGGAGAAAGAGGAGAGCCATGCTGCTACCGACGGTCGCTGGCTCCAACCCCGAGCGCCTGCGGGACCAGCCCAGCACTGCCCTCCAGCCCCGGCCTTACGTCACTTCCGTCACCGGGGTCTGTGCCGGCGTCGGCAGGAGGCGGGACCAGGGCGTGGGCGGGGTCAAGTCCGGGAAGCCGCAGGAGGCGGACTCAGGCGCAGCACCCAGCAGTGAGCACGGCGTCGTGCGGTCGGGACCTGGACTTCTGGGTGTGGGAGGAATTTGAGTGCAAAGGTTAAGGTCTTTCAACCTGGCACCCCATTCTGCAATTCTTCTTCCAGTTTTTTTCGGTTTCCTGGGGTTGTGCAAGTTTGCATTAGGCCACAGCCGAGCCACAATCCTTATTTTACTAACTCTTGGACTTCACCTGGTTGTCTTGGAGCCTGACATTTttagaagagaatgagacttcaaaagccatttccagtccctgctttttcatttgaggaacctgagacttagctagtgaaatggtttgtgcagattcccacagcCCAAATCAAATCGGCTTGACCAAGAACTACTTTGTTCTTGGAGAAAAAAACTATTTGCATTACCTTCTCAGCAATTCAGTGTCAAATCAGTTTATCAGGCAGCCTCTCATGAAGAGGTCTGCTCTCTTACCTCTCTGGGTTTGTCTGTTATTTTGCATCTCTCCTATTCCACTGCAGCCACATTGCTAAGTCCTTCAGCGCTTGTGCTCAAACATGCGAATGTCTAATGATCTCACCTGTTTCAATTCTCTGAGTATCATGAACTTTTGTTAAAAattttaaattgcaacacaccttctcctcctccttaccccgccctactgttttttcatggcacttttcaccttgctgtacactataatatacaccttgatatttgttttcttctccttctaaaatgtaagctccgtagagctgacatctttacttgGCACTCAATTAGTATTTGTTGAGTGAAAGACTGCATGATTACTAGTGTTAAGGAAAATTTTTAAAGAGGGAAAATCCTTATAAAGACACTATATAAACTAGAGGTATTATCAGCCAGATCATTTTACTTGTATTAATAAATCTCTTAGCTcagtacttctcaaacttcaacatacatgtgaaccatctggggatcttgataaaatgcagatttggattcagtagttctaattcaggttgggtcttgagattttgtatttcggacaaaatgcacaggggatgctggtgcccctttcaacaggaccacactttgaatCAGAAGAATTTAGCTCAATCTAGACTAAGTTTAGGGAGAATATTTCCTTTGATGTGTTTCTGATGTCCACTATATGAAAGACACCTTCTAGTCGTTGTAAGGATGCAAGGATAAATAACTGATCTTTACCGTTTAGGCGTCTATGGAGTAGGACAAAATATGATATCCAGTTTGTAAACATTTTTGTGGTACTtgtcacaggctgggttaccctggcagtaaactctgaggtcgagattaaggtataaggcattgattgattagggagtgctcttggaataaacgtctgtgaaggggaggtggaggaagcaga

src/test/resources/com/astrazeneca/vardict/integrationtests/NA12878.chr6_137219200-137219700.bam.bai

@@ -2,5 +2,4 @@ Amplicon,hg19.fa,Colo829-18_S3-sort.bam,chr1,933866,934466,933866,934466,-a 10:0
 Colo829-18_S3-sort	testbed	chr1	934099	934099	G	C	4	4	0	0	2	2	C/C	1.0000	0;2	50.0	1	32.8	1	60.0	3.000	1.0000	0	0	3.000	1	4.0	3	3	CAACGCGGGGGCAGAGGGCG	GTGCGCATGCGGGGCTGCAG	chr1:933867-934466	SNV	1	1	0	0	C:4:F-2:R-2:1.000:2:50.0:true:32.8:true:1.000:60.0:3.0	Good0 4 4 0 0 2 2 C/C 1.0000 0;2 50.0 1 32.8 1 60.0 3.000 1.0000 0 chr1:933867-934466
 Colo829-18_S3-sort	testbed	chr1	934106	934106	A	G	4	2	1	0	1	1	A/G	0.5000	0;2	60.0	0	41.0	0	60.0	4.000	0.6667	0	0	1.000	1	3.5	2	3	GGGGCAGAGGGCGGGTGCGC	TGCGGGGCTGCAGGGATGCG	chr1:933867-934466	SNV	1	1	0	0	A:1:F-1:R-0:0.250:0:40.0:false:41.0:false:0.333:60.0:2.0 & G:2:F-1:R-1:0.500:2:60.0:false:41.0:false:0.667:60.0:4.0 & G&G:1:F-0:R-1:0.250:0:41.0:false:19.5:false:0.000:60.0:0.0	Good0 4 2 1 0 1 1 A/G 0.5000 0;2 60.0 0 41.0 0 60.0 4.000 0.6667 0 chr1:933867-934466
 Colo829-18_S3-sort	testbed	chr1	934144	934144	C	G	8	6	0	0	2	4	G/G	0.7500	0;2	17.0	1	36.7	1	60.0	12.000	0.6000	0	0	2.000	1	2.8	6	10	GCGGAGGGGAGGGCGCGGAG	GGAGGGCGCGGAGCGGAGGG	chr1:933867-934466	SNV	1	1	0	1	G:6:F-2:R-4:0.750:2:17.0:true:36.7:true:0.600:60.0:12.0 & I+GGAGG:2:F-1:R-1:0.250:2:22.0:false:31.5:true:0.100:60.0:1.0 & I+GGAGGGCGCGGAGCGGAGGGGAGGGCGCGGAGCGGAGG:3:F-1:R-2:0.375:2:35.3:true:35.2:true:0.300:60.0:6.0	Good0 8 6 0 0 2 4 G/G 0.7500 0;2 17.0 1 36.7 1 60.0 12.000 0.6000 0 chr1:933867-934466
-Colo829-18_S3-sort	testbed	chr1	934144	934182	C	CGGAGGGCGCGGAGCGGAGGGGAGGGCGCGGAGCGGAGG	8	3	0	0	1	2	G/+38	0.3750	0;2	35.3	1	35.2	1	60.0	6.000	0.3000	0.3750	21	4.000	1	4.3	3	10	GCGGAGGGGAGGGCGCGGAG	GGAGGGCGCGGAGCGGAGGG	chr1:933867-934466	Insertion	1	1	0	1	G:6:F-2:R-4:0.750:2:17.0:true:36.7:true:0.600:60.0:12.0 & I+GGAGG:2:F-1:R-1:0.250:2:22.0:false:31.5:true:0.100:60.0:1.0 & I+GGAGGGCGCGGAGCGGAGGGGAGGGCGCGGAGCGGAGG:3:F-1:R-2:0.375:2:35.3:true:35.2:true:0.300:60.0:6.0	Good0 8 3 0 0 1 2 G/+38 0.3750 0;2 35.3 1 35.2 1 60.0 6.000 0.3000 0.3750 chr1:933867-934466
-
+Colo829-18_S3-sort	testbed	chr1	934144	934144	C	CGGAGGGCGCGGAGCGGAGGGGAGGGCGCGGAGCGGAGG	8	3	0	0	1	2	G/+38	0.3750	0;2	35.3	1	35.2	1	60.0	6.000	0.3000	0.3750	21	4.000	1	4.3	3	10	GCGGAGGGGAGGGCGCGGAG	GGAGGGCGCGGAGCGGAGGG	chr1:933867-934466	Insertion	1	1	0	1	G:6:F-2:R-4:0.750:2:17.0:true:36.7:true:0.600:60.0:12.0 & I+GGAGG:2:F-1:R-1:0.250:2:22.0:false:31.5:true:0.100:60.0:1.0 & I+GGAGGGCGCGGAGCGGAGGGGAGGGCGCGGAGCGGAGG:3:F-1:R-2:0.375:2:35.3:true:35.2:true:0.300:60.0:6.0	Good0 8 3 0 0 1 2 G/+38 0.3750 0;2 35.3 1 35.2 1 60.0 6.000 0.3000 0.3750 chr1:933867-934466