test.vcfwriter source code

1 module test.vcfwriter;
2 
3 import std.stdio;
4 
5 import dhtslib.vcf;
6 import dhtslib.htslib.vcf;
7 
8 int main()
9 {
10     writeln("dhtslib ⚡ VCFWriter");
11 
12     VCFWriter w = VCFWriter("output.vcf");
13 
14     w.addHeaderLineRaw("##source=dhtslib-vcfwriterV0.4");
15     w.addHeaderLineKV("phasing", "none");
16     w.addHeaderLineKV("contig", "<ID=chr3,length=999999,assembly=hg19>");
17     //w.addSample("SAMPLE01");
18 
19     // These should be equivalent: raw htslib call, templated fn
20     bcf_hdr_append(w.vcfhdr.hdr, "##FILTER=<ID=triallelic,Description=\"Triallelic site\">");
21     w.addTag!"FILTER"("noisy", "Noisy region");
22 
23     w.addTag!"INFO"("NS", "1", "Integer", "Number of Samples With Data");
24     w.addTag!"INFO"("XFL", "1", "Float", "Floating point number(s)");
25     w.addTag!"INFO"("XF", "1", "Flag", "Bool something something mumble");
26 
27     // These should be equivalent: raw htslib call, templated fn with string 2nd param, templated fn with int 2nd param
28     bcf_hdr_append(w.vcfhdr.hdr, "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">");
29     w.addTag!"FORMAT"("DDP", "1", "Integer", "De-Duplicated Read Depth (Diamond Dallas Page)");
30     w.addTag!"FORMAT"("XDP", 1, "Integer", "X depth");  // pass integer as second param instead of string
31 
32     // Test vector valued tags
33     w.addTag!"FORMAT"("XXX", 2, "Integer", "Array test");
34 
35     w.addSample("Sample1");
36     w.addSample("Sample2");
37 
38     w.writeHeader();
39     auto vcfhdr = w.getHeader();
40 
41     // for genotype/format tag value arrays
42     const int x = 100;
43     const int y = 200;
44     const int z = 300;
45     const int zz= 400;
46 
47     //string[] filters = ["TRIALLELIC", "GOATS"];
48     string[] filters = ["PASS", "triallelic", "nonex"];
49     VCFRecord r = new VCFRecord(vcfhdr, "chr3", 999, "rs321", "C", "T", 40, filters);
50     r.addInfo("NS", 1);
51     r.addInfo("XS", "Hello");
52     r.addInfo("XFL", 2.1);
53     r.addFormat("DP", [x,x] );
54     w.writeRecord(r);
55 
56     r = new VCFRecord(vcfhdr, "chr3", 1001, "", "", "", 30, "");
57     r.setAlleles("A", "G");
58     r.addInfo("XF", true);
59     r.addFormat("DP", [x,x] );
60     w.writeRecord(r);
61 
62     r = new VCFRecord(vcfhdr, "chr3", 1002, "", "", "", 30, "PASS");
63     r.setAlleles("A", "T", "TCGA");
64     r.addFormat("DP", [x,x] );
65     r.addFormat("XDP", [x,y]);
66     w.writeRecord(r);
67 
68     r = new VCFRecord(vcfhdr, "chr3", 1003, "", "A", "G", 30, "PASS");
69     r.addFormat("XXX", [x, y, z, zz]);
70     w.writeRecord(r);
71 
72     r = new VCFRecord(vcfhdr, "chr3", 1004, "", "G", "A", 20, "PASS");
73     r.add!"FORMAT"("DP", [x,y]);
74     //r.addValue!("FORMAT", int)("DP", [x,y]);
75     w.writeRecord(r);
76 /+
77     filters = [];
78     w.addRecord("chr3", 999, "", "C,T", 40, filters);
79     w.addRecord("chr3", 999999, ".", "A,T", 29.5, filters);
80     w.addRecord("chr3", 1000000, ".", "A,AC", 111.222, filters);
81     w.addRecord("chr3", 440, ".", "CG,C", 30, filters);
82 
83     //w.addRecord("chr1", 999, ".", "A,G", 30, filters);
84 
85     writeln(*w.rows[0]);
86 
87     bcf1_t *b = new bcf1_t;
88     b.pos = 111;
89 
90     w.addRecord(b);
91 
92     w.writeFile();
93 +/
94 
95 
96     return 0;
97 }