1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
/*
* Copyright (C) 2011 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include <string>
void testVcfHeader();
const std::string HEADER_LINE="#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003";
const int NUM_SAMPLES = 3;
const std::string SAMPLES[NUM_SAMPLES] = {"NA00001","NA00002","NA00003"};
const int NUM_META_LINES = 18;
const std::string META_LINES[NUM_META_LINES]={
"##fileformat=VCFv4.1",
"##fileDate=20090805",
"##source=myImputationProgramV3.1",
"##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta",
"##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species=\"Homo sapiens\",taxonomy=x>",
"##phasing=partial",
"##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">",
"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">",
"##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">",
"##INFO=<ID=AA,Number=1,Type=String,Description=\"Ancestral Allele\">",
"##INFO=<ID=DB,Number=0,Type=Flag,Description=\"dbSNP membership, build 129\">",
"##INFO=<ID=H2,Number=0,Type=Flag,Description=\"HapMap2 membership\">",
"##FILTER=<ID=q10,Description=\"Quality below 10\">",
"##FILTER=<ID=s50,Description=\"Less than 50% of samples have data\">",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">",
"##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">",
"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">",
"##FORMAT=<ID=HQ,Number=2,Type=Integer,Description=\"Haplotype Quality\">"};
|
