diff --git a/uk/ac/sanger/artemis/components/variant/BCFReader.java b/uk/ac/sanger/artemis/components/variant/BCFReader.java index 70a3841feb43320a88da8f52daf5cd5f94bda07a..712474b5a837e7ca55ed599cef22935c4cb0ed5e 100644 --- a/uk/ac/sanger/artemis/components/variant/BCFReader.java +++ b/uk/ac/sanger/artemis/components/variant/BCFReader.java @@ -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); } } }