Added adjustment method.

Added test case.
Fixed subCnt to Maybe (issue with hicnt for Insertions found on that case).

Author: PolinaBevad

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

@@ -648,10 +648,12 @@ && isHasAndEquals(querySequence.charAt(n), ref, start)
                                     // subCnt(getVariation(hash, inspos, ref.get(inspos).toString()), dir, tp, tmpq,
                                     // Qmean, nm, conf);
                                     if (inspos > position) {
-                                        Variation tv = getVariation(hash, inspos, String.valueOf(querySequence.charAt(n - 1 - (start - 1 - inspos))));
+                                        Variation tv = getVariationMaybe(hash, inspos, querySequence.charAt(n - 1 - (start - 1 - inspos)));
                                         //Substract count.
-                                        subCnt(tv, dir, tp, queryQuality.charAt(n - 1 - (start -1 - inspos)) - 33,
-                                                mappingQuality, nm - nmoff, conf.goodq);
+                                        if (tv != null) {
+                                            subCnt(tv, dir, tp, queryQuality.charAt(n - 1 - (start - 1 - inspos)) - 33,
+                                                    mappingQuality, nm - nmoff, conf.goodq);
+                                        }
                                     }
                                     // #}
                                     // Adjust count if the insertion is at the edge so that the AF won't > 1

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

@@ -629,6 +629,9 @@ else if (dellen < conf.SVMINLEN) {
                     } else {
                         vref.bias = "0;" + vref.bias;
                     }
+
+                    adjustVariantCounts(p, vref);
+
                     if (conf.debug) {
                         StringBuilder sb = new StringBuilder();
                         for (String str : tmp) {
@@ -688,6 +691,33 @@ else if (dellen < conf.SVMINLEN) {
         return tuple(Rlen, vars);
     }
 
+    /**
+     * Adjust variant negative counts of fields FWD, REV, RFC, RRC to zeros and print the information message to console
+     * @param p start position of variant
+     * @param vref variant to adjust
+     */
+    private static void adjustVariantCounts(int p, Variant vref) {
+        String message = "column in variant on position: " + p + " " + vref.refallele + "->" +
+                vref.varallele + " was negative, adjusted to zero.";
+
+        if (vref.rfc < 0 ) {
+            vref.rfc = 0;
+            System.err.println("Reference forward count " + message);
+        }
+        if (vref.rrc < 0) {
+            vref.rrc = 0;
+            System.err.println("Reference reverse count " + message);
+        }
+        if (vref.fwd < 0) {
+            vref.fwd = 0;
+            System.err.println("Variant forward count " + message);
+        }
+        if (vref.rev < 0 ) {
+            vref.rev = 0;
+            System.err.println("Variant reverse count " + message);
+        }
+    }
+
     private static int calcHicov(VariationMap<String, Variation> iv,
                                  VariationMap<String, Variation> v) {
         int hicov = 0;

src/test/resources/com/astrazeneca/vardict/integrationtests/NAP1L1.NegativeRRC.bam

@@ -0,0 +1,11 @@
+Simple,hg38.fa,NAP1L1.NegativeRRC.bam,chr12,76036587,76085033,-f 0.1
+NAP1L1.NegativeRRC	testbed	chr12	76047375	76047375	T	TA	86	43	18	24	19	24	T/+1	0.5000	2;2	41.1	1	35.0	1	60.0	42.000	0.5122	0.0465	0	17.000	1	1.3	42	82	AACCCAAAGAAAATGAATTT	TTTTTTTTTTTTTAAAAGAA	chr12:76036588-76085033	Insertion	0	0
+NAP1L1.NegativeRRC	testbed	chr12	76045954	76045954	C	T	8	8	0	0	4	4	T/T	1.0000	0;2	52.4	1	37.0	0	60.0	16.000	1.0000	0	1	3.000	1	1.1	8	8	AGATAACTCAGAATAATAAC	CAGAATATAACCTATCAGGA	chr12:76036588-76085033	SNV	0	0
+NAP1L1.NegativeRRC	testbed	chr12	76046488	76046488	T	TA	91	16	42	20	9	6	T/+1	0.1758	2;2	38.9	1	37.0	1	60.0	32.000	0.2025	0.0330	11	12.000	1	0.4	16	79	GCATTTCGATGAACTATGGT	AAAAAAAAAAAGCACATAGT	chr12:76036588-76085033	Insertion	0	0
+NAP1L1.NegativeRRC	testbed	chr12	76060186	76060186	G	A	1345	696	304	342	334	362	G/A	0.5175	2;2	42.8	1	36.6	1	54.7	173.000	0.5246	0	0	1.000	1	1.1	692	1319	GCATACTTCCTTTCAAGATC	TGAACTTCCTCATAGAATTT	chr12:76036588-76085033	SNV	0	0
+NAP1L1.NegativeRRC	testbed	chr12	76059796	76059796	A	ACCT	19	3	17	0	1	2	A/+3	0.1579	2;2	41.0	1	37.0	0	40.0	6.000	0.6000	0	2	2.000	1	1.0	3	5	CCAAAATAAAGTTGGTACTA	CCGAAATCTCATCTTCTTCA	chr12:76036588-76085033	Insertion	0	0
+NAP1L1.NegativeRRC	testbed	chr12	76048101	76048102	CA	C	105	17	47	38	9	8	A/-1	0.1619	2;2	39.8	1	36.8	1	60.0	34.000	0.1650	0.0286	13	14.000	1	0.9	17	103	GTTCTTCAAGGAAAAAATTA	AAAAAAAAAAAAAGGTATTT	chr12:76036588-76085033	Deletion	0	0
+NAP1L1.NegativeRRC	testbed	chr12	76056120	76056120	T	C	1439	1434	0	0	559	875	C/C	0.9965	0;2	35.1	1	35.3	1	55.6	31.591	0.9993	0	0	6.000	1	1.3	1390	1391	GGGTCTTCTTTTTCTTCATC	TTTTTCTCATCTTCAATCTT	chr12:76036588-76085033	SNV	0	0
+NAP1L1.NegativeRRC	testbed	chr12	76051637	76051637	C	T	2	2	0	0	1	1	T/T	1.0000	0;2	38.5	1	37.0	0	60.0	4.000	1.0000	0	0	1.000	1	1.0	2	2	CGCCACCAGAGCAGCTGGGA	TACAGGTGCCTGAAGCTGTA	chr12:76036588-76085033	SNV	0	0
+NAP1L1.NegativeRRC	testbed	chr12	76036918	76036918	C	CA	2	2	0	0	1	1	+1/+1	1.0000	0;2	53.2	1	40.2	0	65.2	4.000	1.0000	0	14	15.000	1	1.6	2	2	CCCCGTCTCTACTAAAAATA	AAAAAAAAAAAAAACCCACA	chr12:76036588-76085033	Insertion	0	0
+NAP1L1.NegativeRRC	testbed	chr12	76045879	76045879	A	G	8	4	4	0	1	3	A/G	0.5000	0;2	47.0	1	37.0	0	60.0	8.000	0.5000	0	2	1.000	1	1.5	4	8	AGACTTACTTGGCAGTGTGC	TGGGCTGCTGGAAACTACAA	chr12:76036588-76085033	SNV	0	0