private void MatchingKitsFrm_Load(object sender, EventArgs e)
{
lblKit.Text = kit;
lblName.Text = GGKUtilLib.queryDatabase("kit_master", new string[] { "name" }, "WHERE kit_no='" + kit + "'").Rows[0].ItemArray[0].ToString();
DataTable dt = GGKUtilLib.QueryDB("SELECT cmp_id,kit'Kit No',name'Name',at_longest'Autosomal Longest',at_total'Autosomal Total',x_longest'X Longest',x_total'X Total',mrca'MRCA' FROM (SELECT a.cmp_id,a.kit1'kit',b.name,a.at_longest,a.at_total,a.x_longest,a.x_total,a.mrca FROM cmp_status a,kit_master b WHERE a.at_total!=0 AND a.kit1!='" + kit + "' AND a.kit2='" + kit + "' AND a.status_autosomal=1 AND b.kit_no=a.kit1 AND b.disabled=0 UNION SELECT a.cmp_id,a.kit2'kit',b.name,a.at_longest,a.at_total,a.x_longest,a.x_total,a.mrca FROM cmp_status a,kit_master b WHERE a.at_total!=0 AND a.kit2!='" + kit + "' AND a.kit1='" + kit + "' AND a.status_autosomal=1 AND b.kit_no=a.kit2 AND b.disabled=0) ORDER BY at_longest DESC,at_total DESC");
dgvMatches.Columns.Clear();
dgvMatches.DataSource = dt;
dgvMatches.Columns[0].Visible = false;
dgvMatches.Columns[1].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvMatches.Columns[2].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvMatches.Columns[3].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvMatches.Columns[4].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvMatches.Columns[5].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvMatches.Columns[6].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvMatches.Columns[7].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
DataGridViewCellStyle style = new DataGridViewCellStyle();
style.Format = "N2";
dgvMatches.Columns[3].DefaultCellStyle = style;
dgvMatches.Columns[4].DefaultCellStyle = style;
dgvMatches.Columns[5].DefaultCellStyle = style;
dgvMatches.Columns[6].DefaultCellStyle = style;
}
void bWorker_DoWork(object sender, DoWorkEventArgs e)
{
string[] o = (string[])e.Argument;
string cmp_id = o[0];
string kit2 = o[1];
string name2 = o[2];
segment_dt = GGKUtilLib.QueryDB("select chromosome'Chromosome',start_position'Start Position',end_position'End Position',segment_length_cm'Segment Length (cM)',snp_count'SNP Count',segment_id from cmp_autosomal where cmp_id='" + cmp_id + "'");
if (GGKUtilLib.isPhased(kit))
{
phased_kit = kit;
unphased_kit = kit2;
phased = true;
}
else if (GGKUtilLib.isPhased(kit2))
{
phased_kit = kit2;
unphased_kit = kit;
phased = true;
}
else
{
phased = false;
}
e.Result = new string[] { kit2, name2 };
}
private void bwROH_DoWork(object sender, DoWorkEventArgs e)
{
DataTable dt = GGKUtilLib.QueryDB("select kit_no,roh_status from kit_master where reference=0 and disabled=0");
string kit = null;
string roh = null;
foreach (DataRow row in dt.Rows)
{
if (bwROH.CancellationPending)
{
break;
}
kit = row.ItemArray[0].ToString();
roh = row.ItemArray[1].ToString();
if (roh == "0")
{
bwROH.ReportProgress(dt.Rows.IndexOf(row) * 100 / dt.Rows.Count, "Runs of Homozygosity for kit #" + kit + " (" + GGKUtilLib.getKitName(kit) + ") - Processing ...");
GGKUtilLib.ROH(kit);
}
else if (roh == "1")
{
bwROH.ReportProgress(dt.Rows.IndexOf(row) * 100 / dt.Rows.Count, "Runs of Homozygosity for kit #" + kit + " (" + GGKUtilLib.getKitName(kit) + ") - Already Exists. Skipping..");
}
}
}
private void bwIChkAndFix_DoWork(object sender, DoWorkEventArgs e)
{
GGKUtilLib.integrityCheckAndFix();
DataTable dt = GGKUtilLib.QueryDB("select * from kit_master where reference=1");
if (dt.Rows.Count == 0)
{
this.Invoke(new MethodInvoker(delegate
{
admixtureToolStripMenuItem.Enabled = false;
}));
}
}
void bWorker2_DoWork(object sender, DoWorkEventArgs e)
{
object[] o = (object[])e.Argument;
dt_alleles = GGKUtilLib.QueryDB("select rsid'RSID',position'Position',kit1_genotype'" + o[0] + " (" + o[1] + ")',kit2_genotype'" + o[2] + " (" + o[3] + ")',match'Match' from cmp_mrca where segment_id='" + o[4] + "'");
}
private void bwPhaseVisualizer_DoWork(object sender, DoWorkEventArgs e)
{
DataTable dt_existing = GGKUtilLib.QueryDB("select segment_image,segment_xml from cmp_phased where phased_kit='" + phased_kit + "' and match_kit='" + unphased_kit + "' and chromosome='" + chromosome + "' and start_position=" + start_position + " and end_position=" + end_position);
if (dt_existing.Rows.Count > 0)
{
object[] o = dt_existing.Rows[0].ItemArray;
string xml = o[1].ToString();
dt = new DataTable();
MemoryStream ms = new MemoryStream(Encoding.ASCII.GetBytes(xml));
dt.ReadXml(ms);
this.Invoke(new MethodInvoker(delegate
{
dgvSegment.DataSource = dt;
dgvSegment.Columns[0].HeaderText = "Position";
dgvSegment.Columns[1].HeaderText = GGKUtilLib.sqlSafe(GGKUtilLib.getKitName(unphased_kit));
dgvSegment.Columns[2].HeaderText = GGKUtilLib.sqlSafe(GGKUtilLib.getKitName(phased_kit)) + " (Paternal)";
dgvSegment.Columns[3].HeaderText = GGKUtilLib.sqlSafe(GGKUtilLib.getKitName(phased_kit)) + " (Maternal)";
dgvSegment.Columns[0].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[1].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[2].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[3].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[0].ReadOnly = true;
dgvSegment.Columns[1].ReadOnly = true;
dgvSegment.Columns[2].ReadOnly = true;
dgvSegment.Columns[3].ReadOnly = true;
}));
byte[] image_array = (byte[])o[0];
Image img = GGKUtilLib.byteArrayToImage(image_array);
this.Invoke(new MethodInvoker(delegate
{
original = new Bitmap(img, 600, 150);
pbSegment.Image = original;
}));
}
else
{
dt = GGKUtilLib.QueryDB("select a.position,a.genotype,p.paternal_genotype,p.maternal_genotype from kit_autosomal a,kit_phased p where a.kit_no='" + unphased_kit + "' and a.position>" + start_position + " and a.position<" + end_position + " and a.chromosome='" + chromosome + "' and p.rsid=a.rsid and p.kit_no='" + phased_kit + "' order by a.position");
if (dt.Rows.Count > 0)
{
if (this.IsHandleCreated)
{
this.Invoke(new MethodInvoker(delegate
{
dgvSegment.DataSource = dt;
dgvSegment.Columns[0].HeaderText = "Position";
dgvSegment.Columns[1].HeaderText = GGKUtilLib.sqlSafe(GGKUtilLib.getKitName(unphased_kit));
dgvSegment.Columns[2].HeaderText = GGKUtilLib.sqlSafe(GGKUtilLib.getKitName(phased_kit)) + " (Paternal)";
dgvSegment.Columns[3].HeaderText = GGKUtilLib.sqlSafe(GGKUtilLib.getKitName(phased_kit)) + " (Maternal)";
dgvSegment.Columns[0].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[1].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[2].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[3].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgvSegment.Columns[0].ReadOnly = true;
dgvSegment.Columns[1].ReadOnly = true;
dgvSegment.Columns[2].ReadOnly = true;
dgvSegment.Columns[3].ReadOnly = true;
}));
Image img = GGKUtilLib.getPhasedSegmentImage(dt, chromosome);
this.Invoke(new MethodInvoker(delegate
{
original = img;
pbSegment.Image = img;
}));
}
dt.TableName = "cmp_phased";
StringBuilder sb = new StringBuilder();
StringWriter w = new StringWriter(sb);
dt.WriteXml(w, XmlWriteMode.WriteSchema);
string segment_xml = sb.ToString();
SQLiteConnection conn = GGKUtilLib.getDBConnection();
SQLiteCommand cmd = new SQLiteCommand("INSERT INTO cmp_phased(phased_kit,match_kit,chromosome,start_position,end_position,segment_image,segment_xml) VALUES (@phased_kit,@match_kit,@chromosome,@start_position,@end_position,@segment_image,@segment_xml)", conn);
cmd.Parameters.AddWithValue("@phased_kit", phased_kit);
cmd.Parameters.AddWithValue("@match_kit", unphased_kit);
cmd.Parameters.AddWithValue("@chromosome", chromosome);
cmd.Parameters.AddWithValue("@start_position", start_position);
cmd.Parameters.AddWithValue("@end_position", end_position);
byte[] image_bytes = GGKUtilLib.imageToByteArray(original);
cmd.Parameters.Add("@segment_image", DbType.Binary, image_bytes.Length).Value = image_bytes;
cmd.Parameters.AddWithValue("@segment_xml", segment_xml);
cmd.ExecuteNonQuery();
conn.Close();
}
}
}
private void AdmixtureFrm_Load(object sender, EventArgs e)
{
kitLbl.Text = kit + " (" + GGKUtilLib.getKitName(kit) + ")";
DataTable dt = GGKUtilLib.QueryDB("select name,at_total,at_longest,x,y FROM (select b.name,a.at_total,a.at_longest,b.x,b.y from cmp_status a,kit_master b where a.kit1='" + kit + "' and a.kit2=b.kit_no and a.kit2 like 'HGDP%' and a.status_autosomal=1 and a.at_longest<3 and a.at_total!=0 UNION select b.name,a.at_total,a.at_longest,b.x,b.y from cmp_status a,kit_master b where a.kit2='" + kit + "' and a.kit1=b.kit_no and a.kit1 like 'HGDP%' and a.status_autosomal=1 and a.at_longest<3 and a.at_total!=0) ORDER BY at_total DESC");
double total = 0.0;
foreach (DataRow row in dt.Rows)
{
total += double.Parse(row.ItemArray[1].ToString());
}
DataTable adx_table = new DataTable();
adx_table.Columns.Add("Population");
adx_table.Columns.Add("Location");
adx_table.Columns.Add("Total Shared (cM)");
adx_table.Columns.Add("Longest (cM)");
adx_table.Columns.Add("Percentage");
adx_table.Columns.Add("X");
adx_table.Columns.Add("Y");
string population = null;
string location = null;
double at_total = 0.0;
string at_longest = null;
double percentage = 0.0;
string[] data = null;
for (int i = 0; i < dt.Rows.Count; i++)
{
data = dt.Rows[i].ItemArray[0].ToString().Replace("_", " ").Split(new char[] { ',' });
population = data[0];
location = data[1];
at_total = double.Parse(dt.Rows[i].ItemArray[1].ToString());
at_longest = dt.Rows[i].ItemArray[2].ToString();
percentage = (at_total * 100 / total);
adx_table.Rows.Add(new object[] { population, location, at_total, at_longest, percentage.ToString("#0.00"), dt.Rows[i].ItemArray[3], dt.Rows[i].ItemArray[4] });
chart1.Series[0].Points.AddXY(population + ", " + location + " (" + percentage.ToString("#0.00") + "%)", new object[] { percentage });
}
foreach (DataPoint p in chart1.Series[0].Points)
{
p.IsVisibleInLegend = false;
}
dgv_Admixture.Columns.Clear();
dgv_Admixture.DataSource = adx_table;
dgv_Admixture.Columns[0].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgv_Admixture.Columns[1].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgv_Admixture.Columns[2].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgv_Admixture.Columns[3].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgv_Admixture.Columns[4].AutoSizeMode = DataGridViewAutoSizeColumnMode.Fill;
dgv_Admixture.Columns[5].Visible = false;
dgv_Admixture.Columns[6].Visible = false;
int percent = 0;
int x = 0;
int y = 0;
Image img = pbWorldMap.Image;
Graphics g = Graphics.FromImage(img);
plotted.Clear();
foreach (DataRow row in adx_table.Rows)
{
percent = (int)double.Parse(row.ItemArray[4].ToString());
x = int.Parse(row.ItemArray[5].ToString());
y = int.Parse(row.ItemArray[6].ToString());
if (!plotted.Contains(x + ":" + y))
{
if (percent > 50) // plotting 100% is too big and ugly.
{
percent = 50;
}
setHeatMap(g, percent, x, y);
plotted.Add(x + ":" + y);
}
}
g.Save();
pbWorldMap.Image = img;
}
private void bwPhaseVisualizer_DoWork(object sender, DoWorkEventArgs e)
{
DataTable dt2 = GGKUtilLib.QueryDB("select distinct kit_no from kit_phased");
string phased_kit = null;
string unphased_kit = null;
string chromosome = null;
string start_position = null;
string end_position = null;
int percent = 0;
foreach (DataRow row in dt2.Rows)
{
if (bwPhaseVisualizer.CancellationPending)
{
break;
}
phased_kit = row.ItemArray[0].ToString();
percent = dt2.Rows.IndexOf(row) * 100 / dt2.Rows.Count;
bwPhaseVisualizer.ReportProgress(percent, "Phased Segments for kit #" + phased_kit + " (" + GGKUtilLib.getKitName(phased_kit) + ") - Processing ...");
DataTable dt3 = GGKUtilLib.QueryDB("select unphased_kit,chromosome,start_position,end_position FROM (select kit1'unphased_kit',chromosome,start_position,end_position from cmp_autosomal where kit2='" + phased_kit + "' UNION select kit2'unphased_kit',chromosome,start_position,end_position from cmp_autosomal where kit1='" + phased_kit + "') order by cast(chromosome as integer),start_position");
foreach (DataRow row3 in dt3.Rows)
{
if (bwPhaseVisualizer.CancellationPending)
{
break;
}
unphased_kit = row3.ItemArray[0].ToString();
chromosome = row3.ItemArray[1].ToString();
start_position = row3.ItemArray[2].ToString();
end_position = row3.ItemArray[3].ToString();
DataTable exists = GGKUtilLib.QueryDB("select * from cmp_phased where phased_kit='" + phased_kit + "' and match_kit='" + unphased_kit + "' and chromosome='" + chromosome + "' and start_position=" + start_position + " and end_position=" + end_position);
if (exists.Rows.Count > 0)
{
//already exists...
if (!redo_visual)
{
bwPhaseVisualizer.ReportProgress(percent, "Segment [" + GGKUtilLib.getKitName(phased_kit) + ":" + GGKUtilLib.getKitName(unphased_kit) + "] Chr " + chromosome + ": " + start_position + "-" + end_position + ", Already Processed. Skipping ...");
continue;
}
else
{
GGKUtilLib.UpdateDB("DELETE from cmp_phased where phased_kit='" + phased_kit + "'");
}
}
bwPhaseVisualizer.ReportProgress(percent, "Segment [" + GGKUtilLib.getKitName(phased_kit) + ":" + GGKUtilLib.getKitName(unphased_kit) + "] Chr " + chromosome + ": " + start_position + "-" + end_position + ", Processing ...");
DataTable dt = GGKUtilLib.QueryDB("select a.position,a.genotype,p.paternal_genotype,p.maternal_genotype from kit_autosomal a,kit_phased p where a.kit_no='" + unphased_kit + "' and a.position>" + start_position + " and a.position<" + end_position + " and a.chromosome='" + chromosome + "' and p.rsid=a.rsid and p.kit_no='" + phased_kit + "' order by a.position");
if (dt.Rows.Count > 0)
{
if (bwPhaseVisualizer.CancellationPending)
{
break;
}
Image img = GGKUtilLib.getPhasedSegmentImage(dt, chromosome);
dt.TableName = "cmp_phased";
StringBuilder sb = new StringBuilder();
StringWriter w = new StringWriter(sb);
dt.WriteXml(w, XmlWriteMode.WriteSchema);
string segment_xml = sb.ToString();
SQLiteConnection conn = GGKUtilLib.getDBConnection();
SQLiteCommand cmd = new SQLiteCommand("INSERT INTO cmp_phased(phased_kit,match_kit,chromosome,start_position,end_position,segment_image,segment_xml) VALUES (@phased_kit,@match_kit,@chromosome,@start_position,@end_position,@segment_image,@segment_xml)", conn);
cmd.Parameters.AddWithValue("@phased_kit", phased_kit);
cmd.Parameters.AddWithValue("@match_kit", unphased_kit);
cmd.Parameters.AddWithValue("@chromosome", chromosome);
cmd.Parameters.AddWithValue("@start_position", start_position);
cmd.Parameters.AddWithValue("@end_position", end_position);
byte[] image_bytes = GGKUtilLib.imageToByteArray(img);
cmd.Parameters.Add("@segment_image", DbType.Binary, image_bytes.Length).Value = image_bytes;
cmd.Parameters.AddWithValue("@segment_xml", segment_xml);
cmd.ExecuteNonQuery();
conn.Close();
}
}
}
}
private void bwPhasing_DoWork(object sender, DoWorkEventArgs e)
{
if (father_kit != "Unknown" && mother_kit != "Unknown")
{
dt = GGKUtilLib.QueryDB("SELECT c.[rsid]'RSID',c.[chromosome]'Chromosome',c.[position]'Position',c.[genotype]\"Child\",COALESCE(f.[genotype],'--')\"Father\",COALESCE(m.[genotype],'--')\"Mother\",''\"Phased Paternal\",''\"Phased Maternal\" FROM kit_autosomal c left outer join kit_autosomal f,kit_autosomal m on f.rsid=c.rsid AND m.rsid=c.rsid WHERE c.kit_no='" + child_kit + "' AND f.kit_no='" + father_kit + "' AND m.[kit_no]='" + mother_kit + "' ORDER BY cast(c.chromosome as integer),c.position");
}
else if (father_kit != "Unknown" && mother_kit == "Unknown")
{
dt = GGKUtilLib.QueryDB("SELECT c.[rsid]'RSID',c.[chromosome]'Chromosome',c.[position]'Position',c.[genotype]\"Child\",COALESCE(f.[genotype],'--')\"Father\",'--'\"Mother\",''\"Phased Paternal\",''\"Phased Maternal\" FROM kit_autosomal c left outer join kit_autosomal f on f.rsid=c.rsid WHERE c.kit_no='" + child_kit + "' AND f.kit_no='" + father_kit + "' ORDER BY cast(c.chromosome as integer),c.position");
}
else if (father_kit == "Unknown" && mother_kit != "Unknown")
{
dt = GGKUtilLib.QueryDB("SELECT c.[rsid]'RSID',c.[chromosome]'Chromosome',c.[position]'Position',c.[genotype]\"Child\",'--'\"Father\",COALESCE(m.[genotype],'--')\"Mother\" ,''\"Phased Paternal\",''\"Phased Maternal\" FROM kit_autosomal c left outer join kit_autosomal m on m.rsid=c.rsid WHERE c.kit_no='" + child_kit + "' AND m.kit_no='" + mother_kit + "' ORDER BY cast(c.chromosome as integer),c.position");
}
// after phasing...
string child = null;
string father = null;
string mother = null;
string phased_paternal = null;
string phased_maternal = null;
object[] o = null;
string nc = "N";
bool amb = false;
foreach (DataRow row in dt.Rows)
{
o = row.ItemArray;
phased_paternal = "";
phased_maternal = "";
child = o[3].ToString();
father = o[4].ToString();
mother = o[5].ToString();
if (child.Length == 1)
{
child = child + child;
}
//check
if ((father.Replace(child[0].ToString(), "").Replace(child[1].ToString(), "") == father || mother.Replace(child[0].ToString(), "").Replace(child[1].ToString(), "") == mother) && o[1].ToString() != "X" && father != "--" && mother != "--" && child != "--")
{
mutatedRow.Add(dt.Rows.IndexOf(row));
}
amb = false;
if (father == child && child[0] != child[1] && mother == "--")
{
amb = true;
}
else if (mother == child && child[0] != child[1] && father == "--")
{
amb = true;
}
else if (father == child && child[0] != child[1] && mother == child)
{
amb = true;
}
if (amb)
{
ambiguousRow.Add(dt.Rows.IndexOf(row));
nc = getNucleotideCode(child[0].ToString(), child[1].ToString());
row.SetField(6, nc);
row.SetField(7, nc);
phased_paternal = nc;
phased_maternal = nc;
continue;
}
if (child == "--" || child == "??")
{
if (father[0] == father[1] && father == mother && o[1].ToString() != "X")
{
row.SetField(6, father[0].ToString());
row.SetField(7, father[0].ToString());
phased_paternal = father[0].ToString();
phased_maternal = father[0].ToString();
continue;
}
}
if (male && o[1].ToString() == "X")
{
child = child[0].ToString();
if (child == "-" && mother != "--")
{
row.SetField(6, "");
row.SetField(7, mother[0].ToString());
phased_paternal = "";
phased_maternal = mother[0].ToString();
continue;
}
}
else
{
if (child[0] == child[1] && child[0] != '-' && child[0] != '?')
{
row.SetField(6, child[0].ToString());
row.SetField(7, child[0].ToString());
phased_paternal = child[0].ToString();
phased_maternal = child[0].ToString();
continue;
}
}
if (o[1].ToString() != "X")
{
autosomalSingleSNPPhase(child, father, mother, row, ref phased_paternal, ref phased_maternal);
}
else if (o[1].ToString() == "X")
{
if (male)
{
row.SetField(3, child[0].ToString());
row.SetField(4, "");
row.SetField(6, "");
row.SetField(7, child[0].ToString());
phased_paternal = "";
phased_maternal = child[0].ToString();
}
else
{
autosomalSingleSNPPhase(child, father, mother, row, ref phased_paternal, ref phased_maternal);
}
}
if (phased_paternal == "" && phased_maternal != "")
{
phased_paternal = child.Replace(phased_maternal, "");
if (phased_paternal.Length > 0)
{
phased_paternal = phased_paternal[0].ToString();
}
row.SetField(6, phased_paternal);
}
if (phased_maternal == "" && phased_paternal != "")
{
phased_maternal = child.Replace(phased_paternal, "");
if (phased_maternal.Length > 0)
{
phased_maternal = phased_maternal[0].ToString();
}
row.SetField(7, phased_maternal);
}
}
// save to kit_phased
string rsid = null;
string chromosome = null;
string position = null;
bwPhasing.ReportProgress(-1, "Saving Phased Kit " + child_kit + " ...");
SQLiteConnection conn = GGKUtilLib.getDBConnection();
SQLiteCommand cmd = new SQLiteCommand("DELETE FROM kit_phased where kit_no=@kit_no", conn);
cmd.Parameters.AddWithValue("@kit_no", child_kit);
cmd.ExecuteNonQuery();
using (SQLiteTransaction trans = conn.BeginTransaction())
{
foreach (DataRow row in dt.Rows)
{
o = row.ItemArray;
rsid = o[0].ToString();
chromosome = o[1].ToString();
position = o[2].ToString();
phased_paternal = o[6].ToString();
phased_maternal = o[7].ToString();
cmd = new SQLiteCommand("INSERT OR REPLACE INTO kit_phased(kit_no,rsid,chromosome,position,paternal_genotype,maternal_genotype,paternal_kit_no,maternal_kit_no) VALUES(@kit_no,@rsid,@chromosome,@position,@paternal_genotype,@maternal_genotype,@paternal_kit_no,@maternal_kit_no)", conn);
cmd.Parameters.AddWithValue("@kit_no", child_kit);
cmd.Parameters.AddWithValue("@rsid", rsid);
cmd.Parameters.AddWithValue("@chromosome", chromosome);
cmd.Parameters.AddWithValue("@position", position);
cmd.Parameters.AddWithValue("@paternal_genotype", phased_paternal);
cmd.Parameters.AddWithValue("@maternal_genotype", phased_maternal);
if (father_kit == "Unknown")
{
cmd.Parameters.AddWithValue("@paternal_kit_no", "");
}
else
{
cmd.Parameters.AddWithValue("@paternal_kit_no", father_kit);
}
if (mother_kit == "Unknown")
{
cmd.Parameters.AddWithValue("@maternal_kit_no", "");
}
else
{
cmd.Parameters.AddWithValue("@maternal_kit_no", mother_kit);
}
cmd.ExecuteNonQuery();
}
trans.Commit();
}
}