Skip to content
Snippets Groups Projects
Commit eac670d1 authored by tcarver's avatar tcarver
Browse files

name change for genotypeData setter and getter in VCFRecord

parent e108278e
No related branches found
No related tags found
No related merge requests found
......@@ -250,7 +250,7 @@ class BCFReader extends AbstractVCFReader
int nc = (int) (n_alleles * ((float)(((float)n_alleles+1.f)/2.f)));
String fmts[] = VCFRecord.COLON_PATTERN.split( bcfRecord.getFormat() );
bcfRecord.setData( new String[nsamples][fmts.length] );
bcfRecord.setGenoTypeData( new String[nsamples][fmts.length] );
for(int i=0; i<fmts.length; i++)
{
......@@ -261,22 +261,22 @@ class BCFReader extends AbstractVCFReader
if(fmts[i].equals("GT"))
{
for(int j=0; j<nsamples; j++)
bcfRecord.getData()[j][i] = getGTString(str[j]);
bcfRecord.getGenoTypeData()[j][i] = getGTString(str[j]);
}
else if(fmts[i].equals("PL"))
{
String pls[] = getPLString(str, nsamples);
for(int j=0; j<nsamples; j++)
bcfRecord.getData()[j][i] = pls[j];
bcfRecord.getGenoTypeData()[j][i] = pls[j];
}
else if(fmts[i].equals("DP")||fmts[i].equals("SP")||fmts[i].equals("GQ"))
{
for(int j=0; j<nsamples; j++)
bcfRecord.getData()[j][i] = Integer.toString(byteToInt(str[j]));
bcfRecord.getGenoTypeData()[j][i] = Integer.toString(byteToInt(str[j]));
}
else
{
bcfRecord.getData()[0][i] = new String(str);
bcfRecord.getGenoTypeData()[0][i] = new String(str);
}
}
}
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment