public static NexteraManifest GetUpdatedNexteraManifestsWithNewRegions(NexteraManifest manifest, List<RegionStatistics> regionStats)
{
NexteraManifest nexteraManifestsWithNewRegions = new NexteraManifest(manifest);
// create a dictionary for new regions
Dictionary<string, RegionStatistics> regionStatsLookup = new Dictionary<string, RegionStatistics>();
foreach (RegionStatistics regionStat in regionStats)
{
regionStatsLookup.Add(regionStat.RegionName, regionStat);
}
//update the regions
if (nexteraManifestsWithNewRegions.Regions != null && nexteraManifestsWithNewRegions.Regions.Count > 0)
{
var newRegions = new List<NexteraManifest.ManifestRegion>();
foreach (NexteraManifest.ManifestRegion region in nexteraManifestsWithNewRegions.Regions)
{
NexteraManifest.ManifestRegion tmpRegion = new NexteraManifest.ManifestRegion(region);
if (!regionStatsLookup.ContainsKey(region.Name))
continue;
tmpRegion.Start = regionStatsLookup[region.Name].StartPosition;
tmpRegion.End = regionStatsLookup[region.Name].EndPosition;
newRegions.Add(tmpRegion);
}
nexteraManifestsWithNewRegions.Regions = newRegions;
}
return nexteraManifestsWithNewRegions;
}
public static void WriteNexteraManifests(NexteraManifest manifest, TextWriter writer)
{
writer.WriteLine("#{0}: {1}", "Manifest Type", "Regions");
writer.WriteLine("#{0}: {1}", "Target Region Count", manifest.Regions.Count);
writer.WriteLine("#{0}: {1}", "Date", DateTime.Now.ToShortDateString());
writer.WriteLine("[Header]");
//writer.WriteLine("Manifest Version\t1.0");
if (!string.IsNullOrEmpty(manifest.GenomeName))
{
writer.WriteLine("ReferenceGenome\t" + manifest.GenomeName);
}
writer.WriteLine("[Regions]");
List<string> headers = new List<string>();
if (manifest.ColumnNames != null && manifest.ColumnNames.Length > 0)
{
foreach (int columnNumber in manifest.ColumnNumbers)
{
if (columnNumber >= 0 && columnNumber < manifest.ColumnNames.Length)
{
headers.Add(manifest.ColumnNames[columnNumber]);
}
}
writer.WriteLine(string.Join("\t", headers.ToArray()));
}
if (manifest.Regions != null && manifest.Regions.Count > 0)
{
foreach (NexteraManifest.ManifestRegion region in manifest.Regions)
{
NexteraManifest.ManifestRegion tmpRegion = new NexteraManifest.ManifestRegion(region);
List<string> line = new List<string>();
foreach (string header in headers)
{
switch (header.ToLowerInvariant())
{
case "name":
line.Add(tmpRegion.Name);
break;
case "chromosome":
line.Add(tmpRegion.Chromosome);
break;
case "start":
case "amplicon start":
line.Add(tmpRegion.Start.ToString());
break;
case "end":
case "amplicon end":
line.Add(tmpRegion.End.ToString());
break;
case "startprobelength":
case "upstream probe length":
line.Add(tmpRegion.StartProbeLength.ToString());
break;
case "endprobelength":
case "downstream probe length":
line.Add(tmpRegion.EndProbeLength.ToString());
break;
case "groupname":
case "group name":
case "group":
case "ip group":
line.Add(tmpRegion.GroupName);
break;
}
}
writer.WriteLine(string.Join("\t", line.ToArray()));
}
}
}
