Merge pull request #164 from PolinaBevad/f_fix_tcov_zero

Added fix for total coverage in case of candidate deletion on 3'.

Author: pcingola

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

@@ -1011,6 +1011,13 @@ && isHasAndEquals(complement(ref.get(bp + 1)), ref, p5 - 1)) {
                     sv.splits += cnt3;
                     sv.clusters += pairs != 0 ? 1 : 0;
 
+                    if (!cov.containsKey(p3)) {
+                        cov.put(p3, pairs + sc3v.cnt);
+                    }
+                    if (cov.containsKey(bp) && cov.get(bp) < cov.get(p3)) {
+                        cov.put(bp, cov.get(p3));
+                    }
+
                     adjCnt(vref, sc3v, conf);
                     Variation tmp = new Variation();
                     tmp.cnt = pairs;

src/test/resources/com/astrazeneca/vardict/integrationtests/Tcov_zero_SV_DEL_candidate3.bam

@@ -1,3 +1,4 @@
 Simple,GRCh37.fa,NA24385_tcov_empty.bam,chr8,122660146,122660347,-f 0.001
 NA24385_tcov_empty	testbed	8	122660339	122660339	T	A	37	4	21	12	0	4	T/A	0.1081	2;0	56.5	1	40.8	1	60.0	8.000	0.1143	0	0	2.000	1	2.0	4	35	GGTAGGTATTCAAAAGTATT	AAGGTCAATAATTGTGATCT	8:122660147-122660347	SNV	0	0
-NA24385_tcov_empty	testbed	8	122660248	122660248	G	A	44	15	9	20	4	11	G/A	0.3409	2;2	42.1	1	39.3	1	60.0	30.000	0.3659	0	0	1.000	1	1.7	15	41	ACTCTTTATAATCATCTCTC	ATAGTCCTTTCCACAGATGA	8:122660147-122660347	SNV	0	0
+NA24385_tcov_empty	testbed	8	122660248	122660248	G	A	44	15	9	20	4	11	G/A	0.3409	2;2	42.1	1	39.3	1	60.0	30.000	0.3659	0	0	1.000	1	1.7	15	41	ACTCTTTATAATCATCTCTC	ATAGTCCTTTCCACAGATGA	8:122660147-122660347	SNV	0	0
+NA24385_tcov_empty	testbed	8	122660114	122661194	T	<DEL>	3	3	0	0	1	2	-1080/-1080	1.0000	0;2	50.3	1	40.4	1	28.0	6.000	1.0000	1.0000	0	0	0	0.3	3	3	CTCAGGTGATCTACCCACCT	GGCCTCCCAAAGTGCTGGGA	8:122660147-122660347	DEL	0	2-1-1

src/test/resources/com/astrazeneca/vardict/integrationtests/Tcov_zero_SV_DEL_candidate3.bam.bai

@@ -0,0 +1,6 @@
+Simple,hg38.fa,Tcov_zero_SV_DEL_candidate3.bam,chr8,90534611,90620070,-f 0.1
+Tcov_zero_SV_DEL_candidate3	testbed	chr8	90615919	90615919	C	T	2	2	0	0	1	1	T/T	1.0000	0;2	55.5	1	37.0	0	60.0	4.000	1.0000	0	0	4.000	1	1.0	2	2	GTGATATGGACAATAAGGTC	GGGGTGAGGCGGTGTCAGAT	chr8:90534612-90620070	SNV	0	0
+Tcov_zero_SV_DEL_candidate3	testbed	chr8	90617256	90617256	C	T	7	7	0	0	4	3	T/T	1.0000	0;2	42.3	1	37.0	0	60.0	14.000	1.0000	0	1	1.000	1	1.1	7	7	GTTAAGACTTTGAGGGACTG	TGGGAAGGCATGATTGGTTT	chr8:90534612-90620070	SNV	0	0
+Tcov_zero_SV_DEL_candidate3	testbed	chr8	90605762	90645105	T	<DEL>	6	6	0	0	4	2	-39343/-39343	1.0000	0;2	56.8	1	36.7	1	60.0	12.000	1.0000	1.0000	0	0	0	0.5	6	6	TTAATATGAGAGAACTACAG	CTTACCGAAAACACTGCATT	chr8:90534612-90620070	DEL	0	2-4-1
+Tcov_zero_SV_DEL_candidate3	testbed	chr8	90617487	90617487	C	T	3	3	0	0	1	2	T/T	1.0000	0;2	29.3	1	24.3	1	60.0	2.000	1.0000	0	1	1.000	1	1.3	2	2	GATGGTTTTATAAAAGGGAG	TCCCCTGCACACACTCTCTT	chr8:90534612-90620070	SNV	0	0
+Tcov_zero_SV_DEL_candidate3	testbed	chr8	90615448	90615448	G	A	2	2	0	0	1	1	A/A	1.0000	0;2	45.5	1	37.0	0	60.0	4.000	1.0000	0	0	3.000	1	1.0	2	2	TGTCGTGGGAGGGACCTCGC	GGAGGTAACTGAATCATGGG	chr8:90534612-90620070	SNV	0	0