Added test case and fix position

Author: PolinaBevad

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

@@ -285,7 +285,7 @@ Map<Integer, Integer>, Integer, Double> parseSAM(Region region, String bam,
                     processCigar:
                     //Loop over CIGAR records
                     for (int ci = 0; ci < cigar.numCigarElements(); ci++) {
-                        if (skipOverlappingReads(conf, record, dir, start, mateAlignmentStart)) {
+                        if (skipOverlappingReads(conf, record, position, dir, start, mateAlignmentStart)) {
                             break;
                         }
                         // Length of segment in CIGAR
@@ -318,7 +318,7 @@ Map<Integer, Integer>, Integer, Double> parseSAM(Region region, String bam,
                                         String saTagString = record.getStringAttribute(SAMTag.SA.name());
 
                                         if (m >= 20 && saTagString != null) {
-                                            if (isReadChimericWithSA(record, saTagString, rlen, dir, conf, true)) {
+                                            if (isReadChimericWithSA(record, position, saTagString, rlen, dir, conf, true)) {
                                                 n += m;
                                                 offset = 0;
                                                 // Had to reset the start due to softclipping adjustment
@@ -402,7 +402,7 @@ && isHasAndEquals(querySequence.charAt(m - 1), ref, start - 1)
                                     if (!conf.chimeric) {
                                         String saTagString = record.getStringAttribute(SAMTag.SA.name());
                                         if (m >= 20 && saTagString != null) {
-                                            if (isReadChimericWithSA(record, saTagString, rlen,
+                                            if (isReadChimericWithSA(record, position, saTagString, rlen,
                                                     dir, conf, false)) {
                                                 n += m;
                                                 offset = 0;
@@ -1087,7 +1087,7 @@ && isNotEquals('N', ref.get(start))) {
                                 p++;
                             }
                             // Skip read if it is overlap
-                            if (skipOverlappingReads(conf, record, dir, start, mateAlignmentStart)) {
+                            if (skipOverlappingReads(conf, record, position, dir, start, mateAlignmentStart)) {
                                 break processCigar;
                             }
                         }
@@ -1269,7 +1269,7 @@ private static void addVariationForDeletion(Configuration conf,
         }
     }
 
-    private static boolean isReadChimericWithSA(SAMRecord record, String saTagString, int rlen,
+    private static boolean isReadChimericWithSA(SAMRecord record, int position, String saTagString, int rlen,
                                                 boolean dir, Configuration conf, boolean is5Side){
         String[] saTagArray = saTagString.split(",");
         String saChromosome = saTagArray[0];
@@ -1285,12 +1285,12 @@ private static boolean isReadChimericWithSA(SAMRecord record, String saTagString
 
         boolean isChimericWithSA = ((dir && saDirectionIsForward) || (!dir && !saDirectionIsForward))
                 && saChromosome.equals(record.getReferenceName())
-                && (abs(saPosition - record.getAlignmentStart()) < 2 * rlen)
+                && (abs(saPosition - position) < 2 * rlen)
                 && mm.find();
 
         if (conf.y && isChimericWithSA) {
             System.err.println(record.getReadName() + " " + record.getReferenceName()
-                    + " " + record.getAlignmentStart() + " " + record.getMappingQuality()
+                    + " " + position + " " + record.getMappingQuality()
                     + " " + record.getCigarString()
                     + " is ignored as chimeric with SA: " +
                     saPosition + "," + saDirectionString + "," + saCigar);
@@ -1328,20 +1328,20 @@ private static void appendSegments(String querySequence, String queryQuality, Ci
         }
     }
 
-    private static boolean skipOverlappingReads(Configuration conf, SAMRecord record, boolean dir, int start, int mateAlignmentStart) {
+    private static boolean skipOverlappingReads(Configuration conf, SAMRecord record, int position, boolean dir, int start, int mateAlignmentStart) {
         if (conf.uniqueModeAlignmentEnabled && isPairedAndSameChromosome(record)
                 && !dir && start >= mateAlignmentStart) {
             return true;
         }
         if (conf.uniqueModeSecondInPairEnabled && record.getSecondOfPairFlag() && isPairedAndSameChromosome(record)
-                && isReadsOverlap(record, start, mateAlignmentStart)) {
+                && isReadsOverlap(record, start, position, mateAlignmentStart)) {
             return true;
         }
         return false;
     }
 
-    private static boolean isReadsOverlap(SAMRecord record, int start, int mateAlignmentStart){
-        if (record.getAlignmentStart() >= mateAlignmentStart) {
+    private static boolean isReadsOverlap(SAMRecord record, int start, int position, int mateAlignmentStart){
+        if (position >= mateAlignmentStart) {
             return start >= mateAlignmentStart
                     && start <= (mateAlignmentStart + record.getCigar().getReferenceLength() - 1);
         }

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

@@ -1,6 +1,7 @@
 package com.astrazeneca.vardict.modules;
 
 import com.astrazeneca.vardict.Configuration;
+import com.astrazeneca.vardict.Utils;
 import com.astrazeneca.vardict.collection.Tuple;
 import com.astrazeneca.vardict.collection.VariationMap;
 import com.astrazeneca.vardict.data.Reference;
@@ -183,7 +184,7 @@ public static Tuple.Tuple2<Integer, Map<Integer, Vars>> toVars(Region region,
                 tvref.extrafreq = cnt.extracnt != 0 ? cnt.extracnt / (double) ttcov : 0;
                 tvref.shift3 = 0;
                 tvref.msi = 0;
-                tvref.nm = cnt.nm / (double) cnt.cnt;
+                tvref.nm = Utils.roundHalfEven("0.0", cnt.nm / (double) cnt.cnt);
                 tvref.hicnt = hicnt;
                 tvref.hicov = hicov;
                 tvref.duprate = duprate;
@@ -255,7 +256,7 @@ public static Tuple.Tuple2<Integer, Map<Integer, Vars>> toVars(Region region,
                     tvref.extrafreq = cnt.extracnt != 0 ? cnt.extracnt / (double)ttcov : 0;
                     tvref.shift3 = 0;
                     tvref.msi = 0;
-                    tvref.nm = cnt.nm / (double)cnt.cnt;
+                    tvref.nm = Utils.roundHalfEven("0.0", cnt.nm / (double)cnt.cnt);
                     tvref.hicnt = hicnt;
                     tvref.hicov = hicov;
                     tvref.duprate = duprate;

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

@@ -345,7 +345,7 @@ public static String realignins(Map<Integer, VariationMap<String, Variation>> ha
                             int flag = 0;
                             int offset = (sc3pp - p - 1) % insert.length();
                             String tvn = vn;
-                            for(int seqi = 0; seqi < seq.length() && seqi < insert.length(); seqi++) {
+                            for(int seqi = 0; seqi < seq.length() && seqi + offset < insert.length(); seqi++) {
                                 if (!substr(seq, seqi, 1).equals(substr(insert, seqi + offset, 1))) {
                                     flag++;
                                     tvn = tvn.replace(substr(tvn, seqi + offset + 1, 1), substr(seq, seqi, 1));

src/test/resources/com/astrazeneca/vardict/integrationtests/HCC2218_C_position_bug.bam

@@ -1 +1,2 @@
-11,1278939,1281541,CGGTAAGACGCTGCAGAGCAGAGGTGCCCGGCATAGGGTGAGGGGGGACAGAGCCGGTGCCCACCAGGGGCCTGTGGGTTGGGCACAGGAGAGCAGAGGAGAGCCACTGTGTCCTGGCGTGACCGCGGCAGGACCACTCGGCAGAGATGGCCTCCAGGTGCTTCATTCTCCTCCTAACGATGAGGCTGGTGACCTCTGGCCTGCCCAGGAGTGGCCCAGGGACGTGGGAAGCAGCGGGGAGGTGGCCAAGCAAGGGGCCTGGAGGGAGCCCCCAGGGGCTGTGAAGCGGTCAGGTCCTCGGGGAAAAGCACGCCTGCGACTTACTCTGGGAACAAGTGGTCGGGAGGAGGAGTGAGCAGCGCCCAGACAGTGGCCTCCATCCTCCCGCAGTGTGCAACACAACCACCTGCCCCCAGAGCCTGCCTGTGTGCCCGCCAGGGCAGGAGTCCATCTGCACCCAGGAGGAGGGCGACTGCTGTCCCACCTTCCGCTGCAGTGAGCGGGGCTGGGGCCGGGCTCCTGGGTGGCCTCTTGCTGGGGGTGGGGGAGTGCAGGATGGTGGGGGCGCTGGAGCACATGCTCCCCACCACTTGTCGAGGGCTTAGCTCCCTTTCCTTCCAGGACCTCAGCTGTGTTCGTACAATGGCACCTTCTACGGGGTAAGGGCACAGCAGTGGGTGGGTGTGGCCCTGGGGCCTGAACATGTGTGTGGGATGCCCCGGGGCTCTCTGAGCCCCACTCCTTGTCTTGACATTCCTGCCCTGAGGGCCGATCCGCACAGGGGCCCTGGACACGTCAGAGCTGGGACATGCTTGGGACTCAGGGGCACCTTACGTCGACAGCCATGAGCTCCACAACTGCTGCCTCTGAGAGGTCCCTTCAGGGGCTCCCAGCAACAGCCTGGGGGCAGCACACACTGGCCTGGGGTCCCCGCCTGCCCGCCCAGATTCCTACCCGCCCGGATTCCTGCCTGCCAGATTCCTGCCCCCATGGGGTCTCTGCCCACCCAGATTCCTGCCCACATGGGGTCTCTGCCTGCCCAGATTCCCTGCCCACCTGTGGTCCCTGTGTGCATCAGCTCCCTGCCTGCCTGGGTCCATGCTCAGCCAGGGGTGCATCTATGCTCCATCTGAGGAAGGAACAACTCCCTGCAGGCCCCATTGGGTCATGGGGAGGGGTCCTGGCCCTGTTGCCCCACCAGTGCCCTCAGTGCCACCCTCCCACCCCTTGCAGGTTGGTGCAACCTTCCCAGGCGCCCTTCCCTGCCACATGTGTACCTGCCTCTCTGGGGACACCCAGGACCCAACGGTGCAATGTCAGGAGGATGCCTGCAACAATACTACCTGTCCCCAGGTGAGACCCGAGGCACCTGCCCCCAGGTGAGCCCCCGAGGCACCTGCCCCCAAGTGAGACCCGAGGCACCTGCCCCCAGGTGAGACCTGAGTCACCCGCCCCCAGGTGAGCCCCCGAGGCACCTGCCCCCAGGTGAGTCCCTGAGGCACTTGCCCCCAAGTGAGACCCGAGGCACCTGCCCCCAGGTGAGACCCGAGGCACCTGCCCCCAGGTGAGACCTGAGTCACCTGCCCCCAGGTGAGCCACCAAGGCACCTGCCCCCAAGTGAGACCCGAGGCACCTGCCCCCAGGTGAGCCCACAGCTGCTGGGCAGACCCAGCCCTGAGTCACTTATCCTGGCTCCCTGGGGTTCTCTAGCTCAGCCATTGCTGGGGTCTTGTTTGTTTCCAAAGGGAGGGTATGAAGTAGGAGGATAACTGAGGGGGTCTGGGGGTGGGACAGGACCTGCAGGCTGCTGGGGACAGGGGCTGAGGTCAGGTTCCAGGAAGGCAGGGGTAGGCAGAGAGAAGGTGCTGGAAACTGGGGTGAGGCTGAGCCGGGATAACTGAGTGGGGGCAACTTCTTCGGGTATAGGCCCAGGCAGGGACAGGGCTAAGGGGTCCTGGACCACTGGGGTGTAGACAGGAGGGCAGGCTGGGCCGGGGCATGTGCTGGAGGAGAGGGTTAGGGCCTGACGCCCCTCATGTCCCCACAGGGCTTTGAGTACAAGAGAGTGGCCGGGCAGTGCTGTGGGGAGTGCGTCCAGACCGCCTGCCTCACGCCCGATGGCCAGCCAGTCCAGGTAACAGCAGAGGCATGTGGGGGCAGGTCTCAGCTCCCTCCCTGGAGACCCTCACCCCCAATGGGGCTCTGCACAAGAGGTAATCCCTACTCAGCTTCCACACTCACCCTTGCATTTCAGCTGAATGAAACCTGGGTCAACAGCCATGTGGACAACTGCACCGTGTACCTCTGTGAGGCTGAGGGTGGAGTCCATTTGCTGACCCCACAGCCTGCATCCTGCCCAGATGTGTCCAGCTGCAGGGTGTGTGCTGGAGGCCCTGCCCCTGCCTGGGAGTCCTTGTCCATCAGGGAGGCCCAACCCCTGTCTGGGATGCCCTGCACAGCAGGGAGGCCCCACCCCTGCTGGGGAGGCCCCACCCCTGCCTGGGAAGCCCCACCCCTGCCTGGGAGGCCCCGCCCCTGCCCGGGAGGCCATGCCCCTGCCCGGGTGGGCCCCTCCCCAGGAGGCCGCACCCACCAGGGAGGCC
+11,1278939,1281541,CGGTAAGACGCTGCAGAGCAGAGGTGCCCGGCATAGGGTGAGGGGGGACAGAGCCGGTGCCCACCAGGGGCCTGTGGGTTGGGCACAGGAGAGCAGAGGAGAGCCACTGTGTCCTGGCGTGACCGCGGCAGGACCACTCGGCAGAGATGGCCTCCAGGTGCTTCATTCTCCTCCTAACGATGAGGCTGGTGACCTCTGGCCTGCCCAGGAGTGGCCCAGGGACGTGGGAAGCAGCGGGGAGGTGGCCAAGCAAGGGGCCTGGAGGGAGCCCCCAGGGGCTGTGAAGCGGTCAGGTCCTCGGGGAAAAGCACGCCTGCGACTTACTCTGGGAACAAGTGGTCGGGAGGAGGAGTGAGCAGCGCCCAGACAGTGGCCTCCATCCTCCCGCAGTGTGCAACACAACCACCTGCCCCCAGAGCCTGCCTGTGTGCCCGCCAGGGCAGGAGTCCATCTGCACCCAGGAGGAGGGCGACTGCTGTCCCACCTTCCGCTGCAGTGAGCGGGGCTGGGGCCGGGCTCCTGGGTGGCCTCTTGCTGGGGGTGGGGGAGTGCAGGATGGTGGGGGCGCTGGAGCACATGCTCCCCACCACTTGTCGAGGGCTTAGCTCCCTTTCCTTCCAGGACCTCAGCTGTGTTCGTACAATGGCACCTTCTACGGGGTAAGGGCACAGCAGTGGGTGGGTGTGGCCCTGGGGCCTGAACATGTGTGTGGGATGCCCCGGGGCTCTCTGAGCCCCACTCCTTGTCTTGACATTCCTGCCCTGAGGGCCGATCCGCACAGGGGCCCTGGACACGTCAGAGCTGGGACATGCTTGGGACTCAGGGGCACCTTACGTCGACAGCCATGAGCTCCACAACTGCTGCCTCTGAGAGGTCCCTTCAGGGGCTCCCAGCAACAGCCTGGGGGCAGCACACACTGGCCTGGGGTCCCCGCCTGCCCGCCCAGATTCCTACCCGCCCGGATTCCTGCCTGCCAGATTCCTGCCCCCATGGGGTCTCTGCCCACCCAGATTCCTGCCCACATGGGGTCTCTGCCTGCCCAGATTCCCTGCCCACCTGTGGTCCCTGTGTGCATCAGCTCCCTGCCTGCCTGGGTCCATGCTCAGCCAGGGGTGCATCTATGCTCCATCTGAGGAAGGAACAACTCCCTGCAGGCCCCATTGGGTCATGGGGAGGGGTCCTGGCCCTGTTGCCCCACCAGTGCCCTCAGTGCCACCCTCCCACCCCTTGCAGGTTGGTGCAACCTTCCCAGGCGCCCTTCCCTGCCACATGTGTACCTGCCTCTCTGGGGACACCCAGGACCCAACGGTGCAATGTCAGGAGGATGCCTGCAACAATACTACCTGTCCCCAGGTGAGACCCGAGGCACCTGCCCCCAGGTGAGCCCCCGAGGCACCTGCCCCCAAGTGAGACCCGAGGCACCTGCCCCCAGGTGAGACCTGAGTCACCCGCCCCCAGGTGAGCCCCCGAGGCACCTGCCCCCAGGTGAGTCCCTGAGGCACTTGCCCCCAAGTGAGACCCGAGGCACCTGCCCCCAGGTGAGACCCGAGGCACCTGCCCCCAGGTGAGACCTGAGTCACCTGCCCCCAGGTGAGCCACCAAGGCACCTGCCCCCAAGTGAGACCCGAGGCACCTGCCCCCAGGTGAGCCCACAGCTGCTGGGCAGACCCAGCCCTGAGTCACTTATCCTGGCTCCCTGGGGTTCTCTAGCTCAGCCATTGCTGGGGTCTTGTTTGTTTCCAAAGGGAGGGTATGAAGTAGGAGGATAACTGAGGGGGTCTGGGGGTGGGACAGGACCTGCAGGCTGCTGGGGACAGGGGCTGAGGTCAGGTTCCAGGAAGGCAGGGGTAGGCAGAGAGAAGGTGCTGGAAACTGGGGTGAGGCTGAGCCGGGATAACTGAGTGGGGGCAACTTCTTCGGGTATAGGCCCAGGCAGGGACAGGGCTAAGGGGTCCTGGACCACTGGGGTGTAGACAGGAGGGCAGGCTGGGCCGGGGCATGTGCTGGAGGAGAGGGTTAGGGCCTGACGCCCCTCATGTCCCCACAGGGCTTTGAGTACAAGAGAGTGGCCGGGCAGTGCTGTGGGGAGTGCGTCCAGACCGCCTGCCTCACGCCCGATGGCCAGCCAGTCCAGGTAACAGCAGAGGCATGTGGGGGCAGGTCTCAGCTCCCTCCCTGGAGACCCTCACCCCCAATGGGGCTCTGCACAAGAGGTAATCCCTACTCAGCTTCCACACTCACCCTTGCATTTCAGCTGAATGAAACCTGGGTCAACAGCCATGTGGACAACTGCACCGTGTACCTCTGTGAGGCTGAGGGTGGAGTCCATTTGCTGACCCCACAGCCTGCATCCTGCCCAGATGTGTCCAGCTGCAGGGTGTGTGCTGGAGGCCCTGCCCCTGCCTGGGAGTCCTTGTCCATCAGGGAGGCCCAACCCCTGTCTGGGATGCCCTGCACAGCAGGGAGGCCCCACCCCTGCTGGGGAGGCCCCACCCCTGCCTGGGAAGCCCCACCCCTGCCTGGGAGGCCCCGCCCCTGCCCGGGAGGCCATGCCCCTGCCCGGGTGGGCCCCTCCCCAGGAGGCCGCACCCACCAGGGAGGCC
+chr2,179259252,179261796,GTAAATGGATTTTGGTATCTTTGCTTTTGGCAGTGAAAATATTGAATCGATTTTGCACTTATGAAAAGTTAGTAACTATAAAAAGAAATTTTTTCTACAGCTCTTCTCTTTTCATGGGCAGCAGAAAAGAGTGAGCATCCTGCCCAGAAGGCTCTTTGTCCTTCAGCTGCACTCTTTAGAATGGTGGAAACTGGTTCCCACTCCCTTAGCCAGGGACTGAACCAGACCCCACTGCCCACAAGATCATCCTGGCTTTTATTAGGATTTCATTTTATTTCTATCACACAAAGCTTGTGTGTGTTTAGATTTGGTCTCTCTGTGGTATGATAGTAGGTGATTATTACAGGATTATTTGCAGGATTATATATACATCACACAGATTAATCTGAGGTTTCCAAATGCATCTGTTGCCCTCCAGAGCCAGGACAAAAAGCTCAGGGTAACCTTATCTCCTTTAGACTTGTCCTGTCATTACTGCCCTGGGGTAGAAATGCAGCCTTGCCCTTCAGATGTCTAAAATGTGCTCCTTGGACATGGGCCCAGTAGGGGCTCTTAGAGCTACTGATATTGCATACTTTTAGTGAAGGAGAAAGGATTCTTGTGGGTCTGGGACCTGAAGCTCTTAGTTACAGTATTTGTATATGCTTTATTGGGGGCTATTTACTTTTTACCCCTGCCAGGAGGTAATTTGTTCCTGCCCTGAGTTCCTCTCCCCCTGGCCCTACCTACTTCCATTTCACACATTTAACAACAAAAATGACTTCACTTCCAGTCAAAAATAGTCACATCATCAGTAGCTAGCAGATAAGATACTAACTGGCTTACAAACACTGCTTATATGTCCATGTCTAATCTATAGGAGAGGGTCCTATTTAAGGTTACCTTGATGTGATTCATGACTAATGTTGATGTTTATATTTTCACAGAAAAGTTATTGATGCCAATCAAAGAGAAGCCTGGGTTTCTAACGACACCTACTGGGAGCTTCGAAAGGACCCTGGGTTTAGCAAAGTAGACAGCCCTGTTCTTTGGTAGACTGGGAATGTAGAGCTAGCCAACATATCACATTCTGAATGAATAAATAACTATGCACAATTATGTTTCTTATAGCTATGTGTGGTTTCTGGGTCAACTGAAAACCTACCATTTGCTTTTCTATTCATCTTTATAATGGACTTTCAGAAGTGCATTAGACAAGGCCCCTAACCACTTTGGGATCCTTTCTGTTTTGCTGCAACCATATTCCTTAAAAAAAAAAAAAAAAAAAAAAAAAAAATCCACACCGTCCTTGGAAAGCAGAATAAAAGGAGCAGAATATAAAATCCAAAGTCTGACCAGTTTGTAAAGAAAAACAAATGGTAACTGGTGCTTAAAGCTGATCAAGAAAGTTAACAACAACATAGAAACCACACGATTGTTCCACTGTCTGGAAGCACCATCCCCTATCGCAGGACTCCTGGGCCACAAGCAGTCGGTCAGTGCAGACTTCAAGTGTGTCTGTTTGATGTGGTGTGATTGTGCTGGCCTTGTCGAAAAAGATGTGATGCTTCTCAGAACCTGTTCCATCTGTATGCCATTGTTCATGCCTTAAGAAATGCAAAGATGTACAATAAATCATTTTTAAAATGTGTGCTCATAGGTTTATGTGAAGAACAGATTTTTTGAATCATGGCATGATTCACTTTCTCAATCAGGACAATTATGAGACTAACTTAAATGGGTTTTTTAAAAGTGAACAACACGTGCTTTACTCTGATAAGTCAGTTACCATATGGTATGTCTGAAGGGAAAGAAGGAAAAGACGTGCTAAGTAGATCTCTGTATTTACGTGGCTCGTTAATTTCCTGTCCTGCGTCCAGATAATAAACCATCCCTCTTCCACCTAACCTCACAGTGTGCCCTATTATTTGGAAAAATCTGTCTTTGATTTGGACATTTGGTCATCAGTGTTAAAACCTTAAAAGGAAATAACAAAAAGCATATGGAATTCCTGTGTGGGCTTAGTAGTACTATAAATGTAATTGTTTTTGAGTGAAGCACCATGTAATCCATGTCTCAATCCCATGCCCGCTCCACTGACACTAGTCGAATTCCACTGAGAACAGAAGCAAGAATAATAGTAGTTTATTTGCATTGTTTAAATGAATTCTATGCAAAATCATATTTCAAATTTTCATCAAGTGATTCCATATGGTACATGGCTACATATTAAGCATTTACCTTGCTATTGGCAGAGATATGAAACTTAAGCTAAGGAATGTATCCATCCCAAAGCAGGAAAGCAGAAGTGTGTTTTGCATACTTCAGGATTTGTTTTTCCTCCACTAATATACAGAGGCTTTTGCAGAAAACTTGCATCAGTATTCCTGTTTCTGCACGTAGGTGACTATATAAATGCCTGTATGTTTTTTTTAAAATATCTCCTCAGAGATTTTCCTAGGGAATTATAAAATTACATATATTTTATTGTTAGTTAGATGTTTATTCTTGGATTCTTACCATTAGAATTTAAGTGTTATTTAAAACTCTGATACAGTTACAGACA

src/test/resources/com/astrazeneca/vardict/integrationtests/HCC2218_C_position_bug.bam.bai

@@ -0,0 +1,2 @@
+Simple,GRCh37.fa,HCC2218_C_position_bug.bam,chr2,179260451,179260596,-f 0.001
+HCC2218_C_position_bug	testbed	chr2	179260528	179260529	TC	AA	137	2	10	104	2	0	TCCC/AA	0.0146	2;0	16.5	1	23.0	1	60.0	4.000	0.0183	0	0	2.000	1	5.5	2	109	AAAAAAAAAAAAAAAAAAAA	CACACCGTCCTTGGAAAGCA	chr2:179260452-179260596	Complex	0	0

testdata/fastas/GRCh37.fa.csv

@@ -4,7 +4,7 @@ Colo829-18_S3-sort	testbed	chr1	755941	755941	G	A	14	2	7	4	1	1	G/A	0.1429	2;2	32
 Colo829-18_S3-sort	testbed	chr1	755953	755953	A	G	14	2	6	6	1	1	A/G	0.1429	2;2	22.0	0	41.0	0	48.0	4.000	0.1818	0	2.0	14	0	6	8	0	0	A/A	0	2;0	42.2	1	32.4	1	60.0	3.667	1.0000	0	1.4	1	2.000	1	AGATCCACGCTATCTACACT	CCTGCCTGGCCAGCAGATCC	chr1:755918-756517	StrongSomatic	SNV	0	0	0	0
 Colo829-18_S3-sort	testbed	chr1	756011	756011	A	C	12	0	3	9	0	0	A/A	0	2;0	42.1	1	23.0	1	60.0	0.714	1.0000	0	1.9	15	3	4	8	2	1	A/C	0.2000	2;2	27.0	1	34.7	1	15.0	2.000	0.2000	0	4.7	0	2.000	2	TGCTTGTCCAGCAGGTCCAC	CTGTCTACACTACCTGCCTG	chr1:755918-756517	StrongLOH	SNV	0	0	0	0
 Colo829-18_S3-sort	testbed	chr1	756019	756019	C	T	9	0	2	7	0	0	C/C	0	2;0	55.7	1	37.7	1	60.0	18.000	1.0000	0	2.1	15	3	4	8	1	2	C/T	0.2000	2;2	20.0	1	28.3	1	21.7	2.000	0.1429	0	3.0	1	1.000	1	CAGCAGGTCCACACTGTCTA	ACTACCTGCCTGTCCAGCAG	chr1:755918-756517	StrongLOH	SNV	0	0	0	0
-Colo829-18_S3-sort	testbed	chr1	756217	756259	GCATCCTGTCTTCACTACCTGCTTGTCCAGCAGGTCCACCATG	CCACACTA	7	2	3	2	2	0	GATG/-40CCAiCACTA	0.2857	2;0	9.0	1	37.6	1	60.0	6.000	0.2707	0.2693	2.5	13	3	5	3	2	1	GATG/-40CCAiCACTA	0.2308	2;2	61.0	1	35.8	1	38.0	6.000	0.3750	0.1538	2.7	0	2.000	1	TACCTGCCTGGCCAGTAGAT	TCTACACTGCCTGCCTGGCC	chr1:755918-756517	Germline	Complex	0	0	0	0
+Colo829-18_S3-sort	testbed	chr1	756217	756259	GCATCCTGTCTTCACTACCTGCTTGTCCAGCAGGTCCACCATG	CCACACTA	7	2	3	2	2	0	GATG/-40CCAiCACTA	0.2857	2;0	9.0	1	37.6	1	60.0	6.000	0.2707	0.2693	2.4	13	3	5	3	2	1	GATG/-40CCAiCACTA	0.2308	2;2	61.0	1	35.8	1	38.0	6.000	0.3750	0.1538	2.7	0	2.000	1	TACCTGCCTGGCCAGTAGAT	TCTACACTGCCTGCCTGGCC	chr1:755918-756517	Germline	Complex	0	0	0	0
 Colo829-18_S3-sort	testbed	chr1	756268	756268	G	A	17	1	10	6	1	0	G/A	0.0588	2;0	41.0	0	37.0	0	50.0	2.000	0.0714	0	5.0	13	4	5	4	1	3	G/A	0.3077	2;2	28.8	1	36.5	1	55.0	8.000	0.3333	0	4.0	2	2.000	1	AGGTCCACCATGTCTACACT	CCTGCCTGGCCAGCAGATCC	chr1:755918-756517	Germline	SNV	0	0	0	0
 Colo829-18_S3-sort	testbed	chr1	756285	756285	A	G	17	0	9	6	0	0	A/A	0	2;0	33.3	1	37.0	1	54.4	6.500	1.0000	0	2.3	14	2	5	6	1	1	A/G	0.1429	2;2	5.5	1	41.0	0	60.0	4.000	0.1667	0	7.0	3	1.000	1	ACTGCCTGCCTGGCCAGCAG	TCCACCCTGTCTACACTACC	chr1:755918-756517	StrongLOH	SNV	0	0	0	0
 Colo829-18_S3-sort	testbed	chr1	756285	756320	ATCCACCCTGTCTACACTACCTGCTTGTCCAGCAGG	A	18	4	7	6	3	1	T/-35	0.2222	2;2	61.0	1	41.0	0	55.8	8.000	0.2500	0	1.5	14	2	5	7	1	1	T/-35	0.1429	2;2	60.5	1	39.0	1	47.5	4.000	0.1538	0	1.0	23	2.000	1	ACTGCCTGCCTGGCCAGCAG	TCCACCCTGTCTACACTACC	chr1:755918-756517	Germline	Deletion	0	0	0	0
@@ -17,4 +17,3 @@ Colo829-18_S3-sort	testbed	chr1	756320	756320	G	A	15	5	2	4	3	2	G/A	0.3333	2;2	31
 Colo829-18_S3-sort	testbed	chr1	756380	756380	T	A	11	2	6	3	1	1	T/A	0.1818	2;2	37.0	1	31.5	1	60.0	1.000	0.1429	0	1.5	15	2	7	6	1	1	T/A	0.1333	2;2	42.0	1	39.0	1	60.0	4.000	0.1333	0	2.0	0	2.000	1	CCCTGTCTACACTACCTGGC	GGCCAGTAGATCCACGCTAT	chr1:755918-756517	Germline	SNV	0	0	0	0
 Colo829-18_S3-sort	testbed	chr1	756434	756434	G	C	10	9	0	1	5	4	G/C	0.9000	0;2	25.2	1	40.1	1	60.0	18.000	0.9000	0	2.7	10	10	0	0	6	4	C/C	1.0000	0;2	41.8	1	36.5	1	60.0	9.000	1.0000	0	3.8	1	1.000	1	CTGTCCAGCAGATCCAACCT	TCTATACTACCTGCCTGTCG	chr1:755918-756517	Germline	SNV	0	0	0	0
 Colo829-18_S3-sort	testbed	chr1	756479	756479	C	A	13	12	1	0	8	4	C/A	0.9231	0;2	46.5	1	26.7	1	60.0	1.400	0.8750	0	2.3	10	8	2	0	5	3	C/A	0.8000	0;2	40.4	1	25.8	1	60.0	1.667	0.7143	0	3.4	0	2.000	1	GATCCACCCTGTCTATACTA	CTGCCTGTCCAGCAGGTCCA	chr1:755918-756517	Germline	SNV	0	0	0	0
-