public void processFile(string input_file)
{
SortedDictionary <int, string>[][] chr_v4 = null;
string[] files = Directory.GetFiles(data_files_folder);
int total = files.Length;
Program.addLog("Input file : " + input_file);
DateTime start = DateTime.Now;
int count = 0;
start = DateTime.Now;
ParallelOptions options = new ParallelOptions();
options.MaxDegreeOfParallelism = Environment.ProcessorCount;
chr_v4 = new CompareUtil().NormalizeData(input_file);
Object lockobj = new Object();
Parallel.For(0, files.Length, options, i =>
{
count++;
try
{
lock (lockobj)
{
if (Path.GetFileNameWithoutExtension(files[i]) != Path.GetFileNameWithoutExtension(input_file))
{
if (!(File.Exists(out_folder + Path.GetFileNameWithoutExtension(input_file) + "-" + Path.GetFileNameWithoutExtension(files[i])) ||
File.Exists(out_folder + Path.GetFileNameWithoutExtension(files[i]) + "-" + Path.GetFileNameWithoutExtension(input_file))))
{
CompareTask task = new CompareTask(data_files_folder, out_folder, snp_threshold, base_pairs_threshold, files[i], chr_v4, input_file);
task.doCompare();
}
}
}
}
catch (Exception) { }
Program.addLog(count + " / " + total + ", Remaining: " + (int)(((DateTime.Now.Subtract(start).TotalSeconds / count) * (total - count)) / 60) + " mins. ");
});
}
public void doCompare()
{
//Console.WriteLine("Comparing .." + Path.GetFileName(fv3));
ArrayList output_text = new ArrayList();
StringBuilder sb_result = new StringBuilder();
ArrayList chr_rm = new ArrayList();
output_text.Clear();
SortedDictionary <int, string>[][] chr_v3 = new CompareUtil().NormalizeData(fv3);
chr_rm.Clear();
for (int i = 0; i < 23; i++)
{
if (chr_v3[0][i] == null || chr_v4[0][i] == null)
{
continue;
}
chr_rm.Clear();
foreach (int position in chr_v3[0][i].Keys)
{
if (!chr_v4[0][i].ContainsKey(position)) //these SNPs are not tested.. on the other match
{
chr_rm.Add(position);
}
}
//foreach (int position in chr_rm)
// chr_v4[0][i].Add(position, chr_v3[0][i][position]);
foreach (int position in chr_rm)
{
chr_v4[0][i].Add(position, "--");
}
}
//
int segment_start = 0;
int segment_end = 0;
double total_mb = 0;
int snp_count = 0;
string genotype_v3 = null;
string genotype_v4 = null;
List <int> keys = null;
string rsid = null;
List <string> shared = new List <string>();
int last_success_position = 0;
string file = null;
for (int i = 0; i < 23; i++)
{
if (chr_v3[0][i] == null || chr_v4[0][i] == null)
{
continue;
}
//
snp_count = 0;
keys = chr_v3[0][i].Keys.ToList();
segment_start = -1;
last_success_position = 0;
shared.Clear();
string shared_gt = null;
int prev_pos = 0;
foreach (int position in keys)
{
if (chr_v3[0][i] == null || chr_v4[0][i] == null) // doesn't exist in file.
{
continue;
}
genotype_v3 = chr_v3[0][i][position];
genotype_v4 = chr_v4[0][i][position];
rsid = chr_v3[1][i][position];
if ((shared_gt = new CompareUtil().getShared(genotype_v3, genotype_v4)) != null && position - prev_pos < 50000)
{
// each position recorded is a snp
if (segment_start == -1)
{
segment_start = position;
shared.Clear();
}
snp_count++;
if (i + 1 == 23)
{
shared.Add(rsid + "\tX\t" + position + "\t" + shared_gt);
}
else
{
shared.Add(rsid + "\t" + (i + 1).ToString() + "\t" + position + "\t" + shared_gt);
}
last_success_position = position;
}
else
{
if (segment_start != -1)
{
segment_end = last_success_position;
total_mb = segment_end - segment_start;
if (snp_count > snp_threshold && total_mb > base_pairs_threshold)
{
file = Path.GetFileNameWithoutExtension(input_file) + "-" + Path.GetFileNameWithoutExtension(fv3);
string file_alt = Path.GetFileNameWithoutExtension(fv3) + "-" + Path.GetFileNameWithoutExtension(input_file);
File.AppendAllLines(out_folder + file, shared);
shared.Clear();
}
}
segment_start = -1;
snp_count = 0;
}
prev_pos = position;
}
///
if (segment_start != -1)
{
segment_end = last_success_position;
total_mb = keys[keys.Count - 1] - segment_start;
if (snp_count > snp_threshold && total_mb > base_pairs_threshold)
{
file = Path.GetFileNameWithoutExtension(input_file) + "-" + Path.GetFileNameWithoutExtension(fv3);
string file_alt = Path.GetFileNameWithoutExtension(fv3) + "-" + Path.GetFileNameWithoutExtension(input_file);
File.AppendAllLines(out_folder + file, shared);
shared.Clear();
}
}
snp_count = 0;
///
}
}
