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Merge pull request #397 from AdamaJava/indel_conf
feat(qannotate): allow the homCutoff option to be used in IndelConfidenceMode
2 parents f5a4ee0 + 2063d43 commit c595a61

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-56
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+134
-56
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‎qannotate/src/au/edu/qimr/qannotate/modes/IndelConfidenceMode.java‎

Lines changed: 40 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@
3434

3535
/**
3636
* @author christix
37-
* annotate whether indel is high, low or zero confidence
37+
* annotate whether indel is high, low, or zero confidence
3838
*
3939
*/
4040
public class IndelConfidenceMode extends AbstractMode{
@@ -47,10 +47,12 @@ public class IndelConfidenceMode extends AbstractMode{
4747
private static final float DEFAULT_SSOI = 0.2f;
4848
public static final int DEFAULT_HOMN = 6;
4949
private final Map<String,BitSet> mask = new HashMap<>();
50+
51+
private int homopolymerCutoff = IndelConfidenceMode.DEFAULT_HOMN;
5052

5153
//filters
5254
private static final String FILTER_REPEAT = "REPEAT";
53-
private static final String DESCRITPION_INFO_CONFIDENCE = "set to HIGH if the variants passed all filter, "
55+
private static final String DESCRIPTION_INFO_CONFIDENCE = "set to HIGH if the variants passed all filter, "
5456
+ "nearby homopolymer sequence base less than six and less than 10% reads contains nearby indel; set to Zero if "
5557
+ "coverage more than 1000, or fallen in repeat region; set to LOW for reminding variants";
5658

@@ -68,36 +70,42 @@ public IndelConfidenceMode(Options options) throws Exception{
6870
input = options.getInputFileName();
6971
output = options.getOutputFileName();
7072
commandLine = options.getCommandLine();
73+
options.getHomoplymersCutoff().ifPresent(i -> homopolymerCutoff = i);
7174

7275
logger.tool("input: " + options.getInputFileName());
7376
logger.tool("mask File: " + options.getDatabaseFileName() );
7477
logger.tool("output annotated records: " + options.getOutputFileName());
7578
logger.tool("logger file " + options.getLogFileName());
7679
logger.tool("logger level " + (options.getLogLevel() == null ? QLoggerFactory.DEFAULT_LEVEL.getName() : options.getLogLevel()));
80+
logger.tool("Homopolymer cutoff (will add to filter if value is greater than or equal to cutoff): " + homopolymerCutoff);
7781

7882
addAnnotation(options.getDatabaseFileName() );
7983
}
8084

8185
/**
82-
* load repeat region into RAM
83-
* @param dbfile
84-
* @throws Exception
85-
*/
86+
* Loads repeat region data from the specified file and populates a BitSet for masking.
87+
* Each line in the file is processed to extract chromosome, start, and end positions,
88+
* which are then used to update the mask data structure.
89+
*
90+
* @param dbfile the path to the file containing repeat regions. The file should consist of lines
91+
* where each line contains chromosome, start, and end positions of the repeat regions.
92+
* @throws IOException if an I/O error occurs while reading the file.
93+
*/
8694
private void loadMask(String dbfile) throws IOException {
8795
//load repeat region to bitset
8896
try(BufferedReader reader = new BufferedReader(new FileReader(dbfile))){
8997
String line;
9098
while (( line = reader.readLine()) != null) {
91-
if ( ! line.startsWith("geno")) {
92-
String[] array = line.split(" ");
93-
//int no = Integer.parseInt(array[0]) - 1;
94-
String chr = IndelUtils.getFullChromosome(array[0]);
95-
96-
int start = Integer.parseInt(array[1]);
97-
int end = Integer.parseInt(array[2]);
98-
99-
mask.computeIfAbsent(chr, (v) -> new BitSet()).set(start,end);
100-
}
99+
if ( ! line.startsWith("geno")) {
100+
String[] array = line.split(" ");
101+
//int no = Integer.parseInt(array[0]) - 1;
102+
String chr = IndelUtils.getFullChromosome(array[0]);
103+
104+
int start = Integer.parseInt(array[1]);
105+
int end = Integer.parseInt(array[2]);
106+
107+
mask.computeIfAbsent(chr, (v) -> new BitSet()).set(start,end);
108+
}
101109
}
102110
}
103111
}
@@ -117,11 +125,11 @@ MafConfidence getConfidence(VcfRecord vcf){
117125
float ssoi = (info.getField(VcfHeaderUtils.INFO_SOMATIC) != null) ?
118126
1 : StringUtils.string2Number(vcf.getInfoRecord().getField(IndelUtils.INFO_SSOI), Float.class);
119127

120-
//check homoplymers
128+
//check homopolymers
121129
int lhomo = (info.getField(VcfHeaderUtils.INFO_HOM) == null)? 1 :
122130
StringUtils.string2Number(info.getField(VcfHeaderUtils.INFO_HOM).split(",")[0], Integer.class);
123131

124-
if(nioc <= DEFAULT_NIOC && lhomo <= DEFAULT_HOMN && ssoi >= DEFAULT_SSOI) return MafConfidence.HIGH;
132+
if(nioc <= DEFAULT_NIOC && lhomo <= homopolymerCutoff && ssoi >= DEFAULT_SSOI) return MafConfidence.HIGH;
125133

126134
} else if (filter.equals(IndelUtils.FILTER_HCOVN) || filter.equals(IndelUtils.FILTER_HCOVT) ||
127135
filter.equals(FILTER_REPEAT) || filter.contains(Constants.SEMI_COLON + FILTER_REPEAT + Constants.SEMI_COLON) ||
@@ -134,7 +142,16 @@ MafConfidence getConfidence(VcfRecord vcf){
134142
}
135143

136144

137-
private boolean isRepeat(VcfRecord vcf){
145+
/**
146+
* Determines if the given VCF record falls within a repeat region.
147+
* It checks the specified chromosome and position range in the associated
148+
* BitSet mask for repeat regions.
149+
*
150+
* @param vcf a {@code VcfRecord} representing the variant call to check for repeat regions.
151+
* This includes details such as chromosome, position, and other metadata.
152+
* @return {@code true} if the variant falls within a repeat region; {@code false} otherwise.
153+
*/
154+
private boolean isRepeat(VcfRecord vcf){
138155

139156
String chr = IndelUtils.getFullChromosome(vcf.getChromosome());
140157
BitSet chrMask = mask.get(chr);
@@ -158,14 +175,14 @@ void addAnnotation(String dbfile) throws IOException {
158175

159176
long count = 0;
160177
long repeatCount = 0;
161-
HashSet<ChrPosition> posCheck = new HashSet<ChrPosition>();
178+
HashSet<ChrPosition> posCheck = new HashSet<>();
162179
try (VcfFileReader reader = new VcfFileReader(input) ;
163180
RecordWriter<VcfRecord> writer = new RecordWriter<>(new File(output )) ) {
164181

165182
//reheader
166183
VcfHeader hd = reader.getVcfHeader();
167184
hd.addFilter(FILTER_REPEAT, DESCRIPTION_FILTER_REPEAT );
168-
hd.addInfo(VcfHeaderUtils.INFO_CONFIDENCE, "1", "String", DESCRITPION_INFO_CONFIDENCE);
185+
hd.addInfo(VcfHeaderUtils.INFO_CONFIDENCE, "1", "String", DESCRIPTION_INFO_CONFIDENCE);
169186
hd = reheader(hd, commandLine ,input);
170187

171188
for(final VcfHeaderRecord record: hd)
@@ -183,8 +200,8 @@ void addAnnotation(String dbfile) throws IOException {
183200
writer.add(vcf);
184201
}
185202
}
186-
logger.info(String.format("outputed %d VCF record, happend on %d variants location.", count , posCheck.size()));
187-
logger.info("number of variants fallen into repeat region is " + repeatCount);
203+
logger.info(String.format("outputted %d VCF records in %d locations.", count , posCheck.size()));
204+
logger.info("number of variants in repeat regions: " + repeatCount);
188205

189206
}
190207

‎qannotate/test/au/edu/qimr/qannotate/modes/IndelConfidenceModeTest.java‎

Lines changed: 94 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,5 @@
11
package au.edu.qimr.qannotate.modes;
22

3-
import static org.junit.Assert.assertEquals;
4-
import static org.junit.Assert.assertTrue;
5-
import static org.junit.Assert.fail;
6-
73
import java.io.BufferedWriter;
84
import java.io.File;
95
import java.io.FileWriter;
@@ -21,6 +17,8 @@
2117

2218
import au.edu.qimr.qannotate.Main;
2319

20+
import static org.junit.Assert.*;
21+
2422
public class IndelConfidenceModeTest {
2523
public static String dbMask = "repeat.mask";
2624
public static String input = "input.vcf";
@@ -37,71 +35,79 @@ public void clear(){
3735
}
3836

3937
@Test
40-
public void InfoTest(){
38+
public void infoTest(){
4139

4240
IndelConfidenceMode mode = new IndelConfidenceMode();
4341

4442
String str = "chr1 11303744 . C CA 37.73 PASS SOMATIC;HOM=5,AGCCTGTCTCaAAAAAAAAAA;NIOC=0.087;SVTYPE=INS;END=11303745 GT:AD:DP:GQ:PL:ACINDEL .:.:.:.:.:0,39,36,0[0,0],0,4,4 0/1:30,10:40:75:75,0,541:7,80,66,8[4,4],1,7,8";
4543
// String str = "chr1 11303744 . C CA 37.73 HOM5 SOMATIC;HOMTXT=AGCCTGTCTCaAAAAAAAAAA;NIOC=0.087;SVTYPE=INS;END=11303745 GT:AD:DP:GQ:PL:ACINDEL .:.:.:.:.:0,39,36,0[0,0],0,4,4 0/1:30,10:40:75:75,0,541:7,80,66,8[4,4],1,7,8";
4644

4745
VcfRecord vcf = new VcfRecord(str.split("\\t"));
48-
assertTrue(mode.getConfidence(vcf) == MafConfidence.HIGH);
46+
assertSame(MafConfidence.HIGH, mode.getConfidence(vcf));
4947

5048
//HOMCNTXT is no longer checked
5149
vcf.setInfo("SOMATIC;HOMCNTXT=9,AGCCTGTCTCaAAAAAAAAAA;SVTYPE=INS;END=11303745");
52-
assertTrue(mode.getConfidence(vcf) == MafConfidence.HIGH);
53-
vcf.setInfo("SOMATIC;HOM=9,AGCCTGTCTCaAAAAAAAAAA;SVTYPE=INS;END=11303745");
54-
assertTrue(mode.getConfidence(vcf) == MafConfidence.LOW);
50+
assertSame(MafConfidence.HIGH, mode.getConfidence(vcf));
51+
vcf.setInfo("SOMATIC;HOM=9,AGCCTGTCTCaAAAAAAAAAA;SVTYPE=INS;END=11303745");
52+
assertSame(MafConfidence.LOW, mode.getConfidence(vcf));
5553

5654

5755
//no homopolymers (repeat)
5856
vcf = new VcfRecord(str.split("\\t"));
5957
vcf.setInfo("SOMATIC;NIOC=0.087;SVTYPE=INS;END=11303745");
60-
assertTrue(mode.getConfidence(vcf) == MafConfidence.HIGH);
58+
assertSame(MafConfidence.HIGH, mode.getConfidence(vcf));
6159

6260
//somatic SSOI
6361
vcf.setInfo("SOMATIC;NIOC=0.087;SSOI=0.1;SVTYPE=INS;END=11303745");
64-
assertTrue(mode.getConfidence(vcf) == MafConfidence.HIGH);
62+
assertSame(MafConfidence.HIGH, mode.getConfidence(vcf));
6563

6664
//germline SSOI high
6765
vcf.setInfo("NIOC=0.087;SSOI=0.2;SVTYPE=INS;END=11303745");
68-
assertTrue(mode.getConfidence(vcf) == MafConfidence.HIGH);
66+
assertSame(MafConfidence.HIGH, mode.getConfidence(vcf));
6967

7068
//germline SSOI low
7169
vcf.setInfo("NIOC=0.087;SSOI=0.1;SVTYPE=INS;END=11303745");
72-
assertTrue(mode.getConfidence(vcf) == MafConfidence.LOW);
70+
assertSame(MafConfidence.LOW, mode.getConfidence(vcf));
7371

7472
//9 base repeat
7573
//vcf.setFilter(IndelUtils.FILTER_HOM + "9");
7674
vcf.setInfo("SOMATIC;HOM=9,AGCCTGTCTCaAAAAAAAAAA;NIOC=0.087;SVTYPE=INS;END=11303745");
77-
assertTrue(mode.getConfidence(vcf) == MafConfidence.LOW);
75+
assertSame(MafConfidence.LOW, mode.getConfidence(vcf));
7876

7977
//no repeat but too many nearby indel
8078
vcf.setInfo("SOMATIC;HOM=5,AGCCTGTCTCaAAAAAAAAAA;NIOC=0.187;SVTYPE=INS;END=11303745");
81-
assertTrue(mode.getConfidence(vcf) == MafConfidence.LOW);
79+
assertSame(MafConfidence.LOW, mode.getConfidence(vcf));
8280

8381

8482
//vcf.setFilter(IndelUtils.FILTER_HOM + "3" );
8583
vcf.setInfo("SOMATIC;HOM=3,AGCCTGTCTCaAAAAAAAAAA;NIOC=0.087;SVTYPE=INS;END=11303745");
86-
assertTrue(mode.getConfidence(vcf) == MafConfidence.HIGH);
84+
assertSame(MafConfidence.HIGH, mode.getConfidence(vcf));
8785

8886
vcf.setFilter(IndelUtils.FILTER_MIN );
89-
assertTrue(mode.getConfidence(vcf) == MafConfidence.LOW);
87+
assertSame(MafConfidence.LOW, mode.getConfidence(vcf));
9088

9189
}
9290

9391

9492
@Test
95-
public void confidenceRealLifeIndel() throws Exception {
93+
public void confidenceRealLifeIndel() {
9694
//chr2 29432822 . C CGCGAATT . HCOVT AC=2;AF=1.00;AN=2;DP=1174;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.98;QD=7.19;SOR=11.114;HOM=0,GGATTTTATCgcgaattTCCAAGCTGA;CONF=ZERO GT:GD:AD:DP:GQ:PL .:.:.:.:.:. 1/1:CGCGAATT/CGCGAATT:0,258:258:99:8481,606,0
9795
VcfRecord vcf1 = new VcfRecord(new String[]{"chr2","29432822",".","C","CGCGAATT",".","HCOVT","AC=2;AF=1.00;AN=2;DP=1174;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.98;QD=7.19;SOR=11.114;HOM=0,GGATTTTATCgcgaattTCCAAGCTGA","GT:GD:AD:DP:GQ:PL"," .:.:.:.:.:.","1/1:CGCGAATT/CGCGAATT:0,258:258:99:8481,606,0"});
9896

99-
IndelConfidenceMode cm =new IndelConfidenceMode();
100-
assertTrue(cm.getConfidence(vcf1) == MafConfidence.ZERO);
97+
IndelConfidenceMode cm = new IndelConfidenceMode();
98+
assertSame(MafConfidence.ZERO, cm.getConfidence(vcf1));
10199
}
100+
@Test
101+
public void confidenceRealLifeIndel2() {
102+
//chr2 29432822 . C CGCGAATT . HCOVT AC=2;AF=1.00;AN=2;DP=1174;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.98;QD=7.19;SOR=11.114;HOM=0,GGATTTTATCgcgaattTCCAAGCTGA;CONF=ZERO GT:GD:AD:DP:GQ:PL .:.:.:.:.:. 1/1:CGCGAATT/CGCGAATT:0,258:258:99:8481,606,0
103+
VcfRecord vcf1 = new VcfRecord(new String[]{"chr2","29432822",".","C","CGCGAATT",".","HCOVT","AC=2;AF=1.00;AN=2;DP=1174;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.98;QD=7.19;SOR=11.114;HOM=0,GGATTTTATCgcgaattTCCAAGCTGA","GT:GD:AD:DP:GQ:PL"," .:.:.:.:.:.","1/1:CGCGAATT/CGCGAATT:0,258:258:99:8481,606,0"});
104+
105+
IndelConfidenceMode cm = new IndelConfidenceMode();
106+
assertSame(MafConfidence.ZERO, cm.getConfidence(vcf1));
107+
}
102108

103109
@Test
104-
public void MaskTest() throws Exception{
110+
public void maskTest() {
105111

106112
try{
107113
createMask();
@@ -118,44 +124,87 @@ public void MaskTest() throws Exception{
118124
i ++;
119125
if(i == 1)
120126
//chr1 53741 . CTT C
121-
assertTrue( re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE).equals( MafConfidence.HIGH.name()));
127+
assertEquals(re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE), MafConfidence.HIGH.name());
122128
else if(i == 2)
123129
//chr1 53742 . C CA
124-
assertTrue( re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE).equals( MafConfidence.HIGH.name()));
130+
assertEquals(re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE), MafConfidence.HIGH.name());
125131
else if(i == 3)
126132
//chr1 53742 . CTT C
127-
assertTrue( re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE).equals( MafConfidence.ZERO.name()));
133+
assertEquals(re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE), MafConfidence.ZERO.name());
128134
else if(i == 4)
129135
//chr1 53743 . C CA
130136
//the insertion happened bwt 53743 and 53744, so it is before repeat region
131-
assertTrue( re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE).equals( MafConfidence.HIGH.name()));
137+
assertEquals(re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE), MafConfidence.HIGH.name());
132138
else if(i == 5)
133139
//chr1 53744 . CTT C
134-
assertTrue( re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE).equals( MafConfidence.ZERO.name()));
140+
assertEquals(re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE), MafConfidence.ZERO.name());
135141
}
136142
assertEquals(5, i);
137143
}
138144

139-
}catch(Exception e){
145+
} catch(Exception e){
140146
System.out.println(e.getMessage());
141-
142-
fail( "My method throw expection" );
147+
fail( "My method threw an exception" );
143148
}
144149

145150
}
151+
152+
@Test
153+
public void homopolymerOptionTest() {
154+
try{
155+
createMask();
156+
createHomVcf();
157+
158+
String[] args ={"--mode","IndelConfidence", "-i", new File(input).getAbsolutePath(), "-o", new File(output).getAbsolutePath(),
159+
"-d", new File(dbMask).getAbsolutePath(), "--log", new File(log).getAbsolutePath()};
160+
Main.main(args);
161+
162+
try (VcfFileReader reader = new VcfFileReader(new File(output))) {
163+
int i = 0;
164+
for ( VcfRecord re : reader) {
165+
if (++i == 1) {
166+
assertEquals(MafConfidence.LOW.name(), re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE));
167+
} else if (i == 2) {
168+
assertEquals(MafConfidence.HIGH.name(), re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE));
169+
}
170+
}
171+
assertEquals(2, i);
172+
}
173+
174+
args = new String[]{"--mode", "IndelConfidence", "-i", new File(input).getAbsolutePath(), "-o", new File(output).getAbsolutePath(),
175+
"-d", new File(dbMask).getAbsolutePath(), "--log", new File(log).getAbsolutePath(), "--homCutoff", "8"};
176+
Main.main(args);
177+
178+
try (VcfFileReader reader = new VcfFileReader(new File(output))) {
179+
int i = 0;
180+
for ( VcfRecord re : reader) {
181+
if (++i == 1) {
182+
assertEquals(MafConfidence.HIGH.name(), re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE));
183+
} else if (i == 2) {
184+
assertEquals(MafConfidence.HIGH.name(), re.getInfoRecord().getField(VcfHeaderUtils.INFO_CONFIDENCE));
185+
}
186+
}
187+
assertEquals(2, i);
188+
}
189+
190+
} catch(Exception e){
191+
System.out.println(e.getMessage());
192+
fail( "My method threw an exception" );
193+
}
194+
}
146195

147196
public static void createMask() throws IOException{
148-
final List<String> data = new ArrayList<String>();
197+
final List<String> data = new ArrayList<>();
149198
data.add("genoName genoStart genoEnd repClass repFamily");
150199
data.add("1 53744 53780 Low_complexity Low_complexity");
151200
data.add("chr1 54712 54820 Simple_repeat Simple_repeat");
152-
try(BufferedWriter out = new BufferedWriter(new FileWriter(dbMask));) {
201+
try(BufferedWriter out = new BufferedWriter(new FileWriter(dbMask))) {
153202
for (final String line : data) out.write(line +"\n");
154203
}
155204
}
156205

157206
public static void createVcf() throws IOException{
158-
final List<String> data = new ArrayList<String>();
207+
final List<String> data = new ArrayList<>();
159208
data.add("##fileformat=VCFv4.0");
160209
data.add(VcfHeaderUtils.STANDARD_UUID_LINE + "=abcd_12345678_xzy_999666333");
161210
data.add("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO");
@@ -166,9 +215,21 @@ public static void createVcf() throws IOException{
166215
data.add("chr1 53743 . C CA 37.73 PASS SOMATIC;HOMCNTXT=5,AGCCTGTCTCaAAAAAAAAAA;NIOC=0.087");
167216
data.add("chr1 53744 . CTT C 37.73 PASS SOMATIC;HOMCNTXT=5,AGCCTGTCTCaAAAAAAAAAA;NIOC=0.087");
168217

169-
try(BufferedWriter out = new BufferedWriter(new FileWriter(input));) {
218+
try(BufferedWriter out = new BufferedWriter(new FileWriter(input))) {
170219
for (final String line : data) out.write(line +"\n");
171220
}
172221

173222
}
223+
public static void createHomVcf() throws IOException{
224+
final List<String> data = new ArrayList<>();
225+
data.add("##fileformat=VCFv4.0");
226+
data.add(VcfHeaderUtils.STANDARD_UUID_LINE + "=abcd_12345678_xzy_999666333");
227+
data.add("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t29ab944c-f37f-4531-95ac-57c52c53be6f\t78ab1438-d237-4cff-a76a-835320a5fb0f");
228+
data.add("chr1\t897580\trs397863599\tAT\tA\t404.73\tPASS\tBaseQRankSum=1.304;ClippingRankSum=0.000;DP=50;ExcessHet=3.0103;FS=2.463;MQ=60.00;MQRankSum=0.000;QD=8.26;ReadPosRankSum=-0.193;SOR=0.751;NIOC=0;SSOI=0.286;SVTYPE=DEL;END=897581;IN=1;VLD;DB;VAF=0.696;HOM=8,GACTCACTGA_TTTTTTTCTA\tGT:AD:DP:G;D:GQ:PL:ACINDEL\t0/1:29,20:49:AT/A:99:442,0,732:14,50,49,14[7,7],18[18],0,0,1\t0/1:10,51:61:AT/A:99:1367,0,121:43,61,61,48[21,27],48[43],0,0,1");
229+
data.add("chr1\t1303675\trs60404130\tC\tCCCT\t1037.73\tPASS\tBaseQRankSum=1.750;ClippingRankSum=0.000;DP=44;ExcessHet=3.0103;FS=13.869;MQ=59.81;MQRankSum=0.000;QD=30.90;ReadPosRankSum=2.125;SOR=1.634;NIOC=0.030;SSOI=0.758;SVTYPE=INS;END=1303676;IN=1;VLD;DB;VAF=0.86;HOM=5,CCTGTTGCCCcctCCTCTTTCTC\tGT:AD:DP:GD:GQ:PL:ACINDEL\t1/1:3,24:27:CCCT/CCCT:72:1075,72,0:23,33,33,25[6,19],28[25],0,1,2\t1/1:5,17:22:CCCT/CCCT:23:537,23,0:18,34,33,18[10,8],21[21],1,1,4");
230+
try(BufferedWriter out = new BufferedWriter(new FileWriter(input))) {
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for (final String line : data) out.write(line +"\n");
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}
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}
174235
}

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