本文整理汇总了C#中System.IO.StreamReader.GetCharpos方法的典型用法代码示例。如果您正苦于以下问题：C# StreamReader.GetCharpos方法的具体用法？C# StreamReader.GetCharpos怎么用？C# StreamReader.GetCharpos使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类System.IO.StreamReader的用法示例。
在下文中一共展示了StreamReader.GetCharpos方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C#代码示例。
示例1: FillDbsnpIdByPosition
/// <summary>
/// Fill dbsnp information. The name of SNPItem will be replaced by dbSNP name and the mapping between dbSNP name and old SNPItem name will be returned.
/// </summary>
/// <param name="snpItems"></param>
/// <param name="dbSnpVcfFile"></param>
/// <param name="progress"></param>
/// <returns></returns>
public static Dictionary<string, string> FillDbsnpIdByPosition(this IEnumerable<SNPItem> snpItems, string dbSnpVcfFile, IProgressCallback progress = null)
{
var sourceDbsnpMap = snpItems.ToDictionary(m => m.Name, m => m.Name);
if (progress == null)
{
progress = new EmptyProgressCallback();
}
var dic = snpItems.ToDoubleDictionary(m => m.Chrom, m => m.Position);
progress.SetMessage("Filling dbSNP id from {0} ...", dbSnpVcfFile);
using (var sr = new StreamReader(dbSnpVcfFile))
{
progress.SetRange(0, sr.BaseStream.Length);
string line;
while ((line = sr.ReadLine()) != null)
{
if (!line.StartsWith("##"))
{
break;
}
}
int linecount = 0;
Dictionary<int, SNPItem> chrMap = null;
int lastChr = -1;
while (line != null)
{
linecount++;
if (linecount % 10000 == 0)
{
progress.SetPosition(sr.GetCharpos());
}
try
{
//make sure it is SNV
if (!line.Contains("VC=SNV"))
{
continue;
}
//Even it marked as SNV, it still could be insertion/deletion
//2 179658175 rs11537855 C CC,CT . . RS=11537855;RSPOS=179658175;dbSNPBuildID=120;SSR=0;SAO=0;VP=0x050100001205000002000110;GENEINFO=TTN:7273;WGT=1;VC=SNV;SLO;NSF;REF;ASP;OTHERKG;NOC
var parts = line.Split('\t');
if (parts[3].Split(',').Any(l => l.Length != 1))
{
continue;
}
if (parts[4].Split(',').Any(l => l.Length != 1))
{
continue;
}
var chr = HumanChromosomeToInt(parts[0]);
var position = int.Parse(parts[1]);
if (lastChr != chr)
{
if (!dic.TryGetValue(chr, out chrMap))
{
continue;
}
lastChr = chr;
}
SNPItem source;
if (!chrMap.TryGetValue(position, out source))
{
continue;
}
if (!source.Name.Equals(parts[2]))
{
sourceDbsnpMap.Remove(source.Name);
sourceDbsnpMap[source.Name] = parts[2];
}
source.DbsnpRefAllele = parts[3][0];
source.DbsnpAltAllele = parts[4][0];
source.DbsnpIsReversed = parts[7].Contains(";RV;");
}
finally
{
line = sr.ReadLine();
}
}
}
//.........这里部分代码省略.........
示例2: DoFillAllele2FrequencyFrom1000Gome
private static void DoFillAllele2FrequencyFrom1000Gome(this IEnumerable<SNPItem> snpItems, string g1000VcfFile, Func<SNPItem, string> keyFunc, IProgressCallback progress = null)
{
if (progress == null)
{
progress = new ConsoleProgressCallback();
}
var dic = snpItems.ToDictionary(m => keyFunc(m));
progress.SetMessage("Filling MAF from {0} ...", g1000VcfFile);
using (var sr = new StreamReader(g1000VcfFile))
{
progress.SetRange(0, sr.BaseStream.Length);
string line;
while ((line = sr.ReadLine()) != null)
{
if (!line.StartsWith("##"))
{
break;
}
}
int linecount = 0;
while ((line = sr.ReadLine()) != null)
{
linecount++;
if (linecount % 10000 == 0)
{
progress.SetPosition(sr.GetCharpos());
}
var parts = line.Split('\t');
var snp = new SNPItem()
{
Chrom = HumanChromosomeToInt(parts[0]),
Position = int.Parse(parts[1]),
Name = parts[2]
};
SNPItem loc;
if (!dic.TryGetValue(keyFunc(snp), out loc))
{
continue;
}
loc.G1000Allele1 = parts[3][0];
var allele2 = parts[4].Split(',');
var frequencies = parts[7].StringAfter("AF=").StringBefore(";").Split(',');
bool bFound = false;
for (int i = 0; i < allele2.Length; i++)
{
if (allele2[i].Length != 1)
{
continue;
}
loc.G1000Allele2 = allele2[i][0];
if (loc.IsSourceAllelesMatchedWithG1000())
{
loc.G1000Allele2Frequency = double.Parse(frequencies[i]);
bFound = true;
break;
}
}
if (!bFound)
{
loc.G1000Allele1 = ' ';
loc.G1000Allele2 = ' ';
loc.G1000Allele2Frequency = 0.0;
}
}
}
progress.SetMessage("Filling MAF finished.");
}