VCFHeader

addFiledate int addFiledate(): Add a filedate= headerline, which is not called out specifically in the spec, but appears in the spec's example files. We could consider allowing a param here.
addFilter deprecated void addFilter(string id, string description): Add FILTER tag (§1.2.3)
addHeaderLine void addHeaderLine(string id, T number, HeaderTypes type, string description, string source, string _version): Add INFO (§1.2.2) or FORMAT (§1.2.4) tag
addHeaderLine void addHeaderLine(string id, string description): Add FILTER tag (§1.2.3)
addHeaderLineKV int addHeaderLineKV(string key, string value): Add a new header line
addHeaderLineRaw int addHeaderLineRaw(string line): Add a new header line -- must be formatted ##key=value
addHeaderRecord int addHeaderRecord(HeaderRecord rec): Add a new header line using HeaderRecord
addSample int addSample(string name): Add sample to this VCF * int bcf_hdr_add_sample(bcf_hdr_t *hdr, const(char) *sample);
copyHeaderLines void copyHeaderLines(bcf_hdr_t* other): copy header lines from a template without overwiting existing lines
dup auto dup(): copy this header
getHeaderRecord HeaderRecord getHeaderRecord(HeaderRecordType linetype, string id): get a header record via ID field
getHeaderRecord HeaderRecord getHeaderRecord(HeaderRecordType linetype, string key, string value): get a header record via a string value pair
getSampleId int getSampleId(string sam): get int index of sample name
getSamples string[] getSamples(): get sample list
removeHeaderLines void removeHeaderLines(HeaderRecordType linetype): Remove all header lines of a particular type
removeHeaderLines void removeHeaderLines(HeaderRecordType linetype, string key): Remove a header line of a particular type with the key
toString string toString(): string representation of header

Properties

nsamples int nsamples [@property getter]: Number of samples in the header
sequences string[] sequences [@property getter]: List of contigs in the header
vcfVersion string vcfVersion [@property getter]: VCF version, e.g. VCFv4.2

Variables

hdr BcfHdr hdr;: Pointer to htslib BCF/VCF header struct; will be freed from VCFHeader dtor

Examples

import std.exception: assertThrown;
import std.stdio: writeln, writefln;

hts_set_log_level(htsLogLevel.HTS_LOG_TRACE);


auto hdr = VCFHeader(bcf_hdr_init("w\0"c.ptr));

hdr.addHeaderLineRaw("##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">");
hdr.addHeaderLineKV("INFO", "<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">");
// ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
hdr.addHeaderLine!(HeaderRecordType.Info)("AF", HeaderLengths.OnePerAltAllele, HeaderTypes.Integer, "Number of Samples With Data");
hdr.addHeaderLineRaw("##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species=\"Homo sapiens\",taxonomy=x>"); // @suppress(dscanner.style.long_line)
hdr.addHeaderLineRaw("##FILTER=<ID=q10,Description=\"Quality below 10\">");


// Exercise header
assert(hdr.nsamples == 0);
hdr.addSample("NA12878");
assert(hdr.nsamples == 1);
assert(hdr.vcfVersion == "VCFv4.2");

1 import std.exception: assertThrown;
2 import std.stdio: writeln, writefln;
3 
4 hts_set_log_level(htsLogLevel.HTS_LOG_TRACE);
5 
6 
7 auto hdr = VCFHeader(bcf_hdr_init("w\0"c.ptr));
8 
9 hdr.addHeaderLineRaw("##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">");
10 hdr.addHeaderLineKV("INFO", "<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">");
11 
12 auto rec = hdr.getHeaderRecord(HeaderRecordType.Info,"ID","NS");
13 assert(rec.recType == HeaderRecordType.Info);
14 assert(rec.key == "INFO");
15 assert(rec.nkeys == 4);
16 assert(rec.keys == ["ID", "Number", "Type", "Description"]);
17 assert(rec.vals == ["NS", "1", "Integer", "\"Number of Samples With Data\""]);
18 assert(rec["ID"] == "NS");
19 
20 assert(rec.idx == 1);
21 
22 writeln(rec.toString);
23 
24 
25 rec = HeaderRecord(rec.convert(hdr.hdr));
26 
27 assert(rec.recType == HeaderRecordType.Info);
28 assert(rec.key == "INFO");
29 assert(rec.nkeys == 4);
30 assert(rec.keys == ["ID", "Number", "Type", "Description"]);
31 assert(rec.vals == ["NS", "1", "Integer", "\"Number of Samples With Data\""]);
32 assert(rec["ID"] == "NS");
33 // assert(rec["IDX"] == "1");
34 // assert(rec.idx == 1);
35 
36 rec = hdr.getHeaderRecord(HeaderRecordType.Info,"ID","NS");
37 
38 assert(rec.recType == HeaderRecordType.Info);
39 assert(rec.getLength == "1");
40 assert(rec.getValueType == HeaderTypes.Integer);
41 
42 rec.idx = -1;
43 
44 rec["ID"] = "NS2";
45 
46 hdr.addHeaderRecord(rec);
47 auto hdr2 = hdr.dup;
48 // writeln(hdr2.toString);
49 
50 rec = hdr2.getHeaderRecord(HeaderRecordType.Info,"ID","NS2");
51 assert(rec.recType == HeaderRecordType.Info);
52 assert(rec.key == "INFO");
53 assert(rec.nkeys == 4);
54 assert(rec.keys == ["ID", "Number", "Type", "Description"]);
55 assert(rec.vals == ["NS2", "1", "Integer", "\"Number of Samples With Data\""]);
56 assert(rec["ID"] == "NS2");
57 
58 assert(rec.idx == 3);
59 
60 rec = HeaderRecord.init;
61 rec.setHeaderRecordType(HeaderRecordType.Generic);
62 rec.key = "source";
63 rec.value = "hello";
64 hdr.addHeaderRecord(rec);
65 
66 rec = hdr.getHeaderRecord(HeaderRecordType.Generic,"source","hello");
67 assert(rec.recType == HeaderRecordType.Generic);
68 assert(rec.key == "source");
69 assert(rec.value == "hello");
70 assert(rec.nkeys == 0);
71 
72 hdr.addHeaderLine!(HeaderRecordType.Filter)("nonsense","filter");
73 
74 rec = hdr.getHeaderRecord(HeaderRecordType.Filter,"ID","nonsense");
75 assert(rec.recType == HeaderRecordType.Filter);
76 assert(rec.key == "FILTER");
77 assert(rec.value == "");
78 assert(rec.getID == "nonsense");
79 assert(rec.idx == 4);
80 
81 hdr.removeHeaderLines(HeaderRecordType.Filter);
82 
83 auto expected = "##fileformat=VCFv4.2\n" ~ 
84     "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">\n"~
85     "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">\n"~
86     "##INFO=<ID=NS2,Number=1,Type=Integer,Description=\"Number of Samples With Data\">\n"~
87     "##source=hello\n"~
88     "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
89 assert(hdr.toString == expected);
90 
91 rec = rec.init;
92 rec.setHeaderRecordType(HeaderRecordType.Contig);
93 rec.setID("test");
94 rec["length"] = "5";
95 
96 hdr.addHeaderRecord(rec);
97 
98 assert(hdr.sequences == ["test"]);
99 hdr.removeHeaderLines(HeaderRecordType.Generic, "source");
100 hdr.addFilter("test","test");
101 expected = "##fileformat=VCFv4.2\n" ~ 
102     "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">\n"~
103     "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">\n"~
104     "##INFO=<ID=NS2,Number=1,Type=Integer,Description=\"Number of Samples With Data\">\n"~
105     "##contig=<ID=test,length=5>\n"~
106     "##FILTER=<ID=test,Description=\"test\">\n"~
107     "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
108 assert(hdr.toString == expected);
109 rec = hdr.getHeaderRecord(HeaderRecordType.Filter,"test");
110 assert(rec.getDescription() == "\"test\"");
111 
112 rec = HeaderRecord.init;
113 rec.setHeaderRecordType(HeaderRecordType.Info);
114 rec.setID("test");
115 rec.setLength(HeaderLengths.OnePerGenotype);
116 rec.setValueType(HeaderTypes.Integer);
117 hdr.addHeaderRecord(rec);
118 
119 rec = hdr.getHeaderRecord(HeaderRecordType.Info,"test");
120 assert(rec.recType == HeaderRecordType.Info);
121 assert(rec.getLength == "G");
122 assert(rec.getID == "test");
123 assert(rec.getValueType == HeaderTypes.Integer);
124 
125 rec = HeaderRecord.init;
126 rec.setHeaderRecordType(HeaderRecordType.Info);
127 rec.setID("test2");
128 rec.setLength(HeaderLengths.OnePerAllele);
129 rec.setValueType(HeaderTypes.Integer);
130 hdr.addHeaderRecord(rec);
131 
132 rec = hdr.getHeaderRecord(HeaderRecordType.Info,"test2");
133 assert(rec.recType == HeaderRecordType.Info);
134 assert(rec.getLength == "R");
135 assert(rec.getID == "test2");
136 assert(rec.getValueType == HeaderTypes.Integer);
137 
138 rec = HeaderRecord.init;
139 rec.setHeaderRecordType(HeaderRecordType.Info);
140 rec.setID("test3");
141 rec.setLength(HeaderLengths.Variable);
142 rec.setValueType(HeaderTypes.Integer);
143 hdr.addHeaderRecord(rec);
144 
145 rec = hdr.getHeaderRecord(HeaderRecordType.Info,"test3");
146 assert(rec.recType == HeaderRecordType.Info);
147 assert(rec.getLength == ".");
148 assert(rec.getID == "test3");
149 assert(rec.getValueType == HeaderTypes.Integer);
150 
151 rec = HeaderRecord.init;
152 rec.setHeaderRecordType(HeaderRecordType.Info);
153 rec.setID("test4");
154 rec.setLength(1);
155 rec.setValueType(HeaderTypes.Flag);
156 hdr.addHeaderRecord(rec);
157 
158 rec = hdr.getHeaderRecord(HeaderRecordType.Info,"test4");
159 assert(rec.recType == HeaderRecordType.Info);
160 assert(rec.getID == "test4");
161 assert(rec.getValueType == HeaderTypes.Flag);
162 
163 rec = HeaderRecord.init;
164 rec.setHeaderRecordType(HeaderRecordType.Info);
165 rec.setID("test5");
166 rec.setLength(1);
167 rec.setValueType(HeaderTypes.Character);
168 hdr.addHeaderRecord(rec);
169 
170 rec = hdr.getHeaderRecord(HeaderRecordType.Info,"test5");
171 assert(rec.recType == HeaderRecordType.Info);
172 assert(rec.getLength == "1");
173 assert(rec.getID == "test5");
174 assert(rec.getValueType == HeaderTypes.Character);
175 
176 rec = HeaderRecord.init;
177 rec.setHeaderRecordType(HeaderRecordType.Info);
178 rec.setID("test6");
179 rec.setLength(HeaderLengths.Variable);
180 rec.setValueType(HeaderTypes.String);
181 hdr.addHeaderRecord(rec);
182 
183 rec = hdr.getHeaderRecord(HeaderRecordType.Info,"test6");
184 assert(rec.recType == HeaderRecordType.Info);
185 assert(rec.getLength == ".");
186 assert(rec.getID == "test6");
187 assert(rec.getValueType == HeaderTypes.String);
188 
189 expected = "##fileformat=VCFv4.2\n" ~ 
190     "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">\n"~
191     "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">\n"~
192     "##INFO=<ID=NS2,Number=1,Type=Integer,Description=\"Number of Samples With Data\">\n"~
193     "##contig=<ID=test,length=5>\n"~
194     "##FILTER=<ID=test,Description=\"test\">\n"~
195     "##INFO=<ID=test,Number=G,Type=Integer>\n"~
196     "##INFO=<ID=test2,Number=R,Type=Integer>\n"~
197     "##INFO=<ID=test3,Number=.,Type=Integer>\n"~
198     "##INFO=<ID=test4,Number=1,Type=Flag>\n"~
199     "##INFO=<ID=test5,Number=1,Type=Character>\n"~
200     "##INFO=<ID=test6,Number=.,Type=String>\n"~
201     "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
202 writeln(hdr.toString);
203 assert(hdr.toString == expected);

VCFHeader

Constructors

Postblit

Members

Functions

Properties

Variables

Examples

Meta

Source