/** * Remove all lines with a VCF version tag from the provided set of header lines */ private void removeVCFVersionLines( final Set<VCFHeaderLine> headerLines ) { final List<VCFHeaderLine> toRemove = new ArrayList<VCFHeaderLine>(); for (final VCFHeaderLine line : headerLines) { if (VCFHeaderVersion.isFormatString(line.getKey())) { toRemove.add(line); } } headerLines.removeAll(toRemove); }
/** * Remove all lines with a VCF version tag from the provided set of header lines */ private void removeVCFVersionLines( final Set<VCFHeaderLine> headerLines ) { final List<VCFHeaderLine> toRemove = new ArrayList<VCFHeaderLine>(); for (final VCFHeaderLine line : headerLines) { if (VCFHeaderVersion.isFormatString(line.getKey())) { toRemove.add(line); } } headerLines.removeAll(toRemove); }
/** * check our metadata for a VCF version tag, and throw an exception if the version is out of date * or the version is not present */ public void loadVCFVersion() { final List<VCFHeaderLine> toRemove = new ArrayList<VCFHeaderLine>(); for (final VCFHeaderLine line : mMetaData) if (VCFHeaderVersion.isFormatString(line.getKey())) { toRemove.add(line); } // remove old header lines for now, mMetaData.removeAll(toRemove); }
public static VCFHeaderVersion getHeaderVersion(String versionLine) { String[] lineFields = versionLine.split("="); if ( lineFields.length != 2 || !isFormatString(lineFields[0].substring(2)) ) throw new TribbleException.InvalidHeader(versionLine + " is not a valid VCF version line"); if ( !isVersionString(lineFields[1]) ) throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version"); return toHeaderVersion(lineFields[1]); }
public static VCFHeaderVersion getHeaderVersion(String versionLine) { String[] lineFields = versionLine.split("="); if ( lineFields.length != 2 || !isFormatString(lineFields[0].substring(2)) ) throw new TribbleException.InvalidHeader(versionLine + " is not a valid VCF version line"); if ( !isVersionString(lineFields[1]) ) throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version"); return toHeaderVersion(lineFields[1]); }
public static VCFHeaderVersion getHeaderVersion(String versionLine) { String[] lineFields = versionLine.split("="); if ( lineFields.length != 2 || !isFormatString(lineFields[0].substring(2)) ) throw new TribbleException.InvalidHeader(versionLine + " is not a valid VCF version line"); if ( !isVersionString(lineFields[1]) ) throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version"); return toHeaderVersion(lineFields[1]); }
if ( VCFHeaderVersion.isFormatString(line.getKey()) ) continue;
if ( VCFHeaderVersion.isFormatString(line.getKey()) ) continue;
if ( VCFHeaderVersion.isFormatString(line.getKey()) ) continue;
@Override public void setHeader(VCFHeader header) { VCFHeaderVersion version = null; // Normally AbstractVCFCodec parses the header and thereby sets the // version field. It gets used later on so we need to set it. for (final VCFHeaderLine line : header.getMetaDataInInputOrder()) { if (VCFHeaderVersion.isFormatString(line.getKey())) { version = VCFHeaderVersion.toHeaderVersion(line.getValue()); break; } } codec.setHeaderAndVersion(header, version); }
@Override public void setHeader(VCFHeader header) { VCFHeaderVersion version = null; // Normally AbstractVCFCodec parses the header and thereby sets the // version field. It gets used later on so we need to set it. for (final VCFHeaderLine line : header.getMetaDataInInputOrder()) { if (VCFHeaderVersion.isFormatString(line.getKey())) { version = VCFHeaderVersion.toHeaderVersion(line.getValue()); break; } } codec.setHeaderAndVersion(header, version); }
if (line.startsWith(VCFHeader.METADATA_INDICATOR)) { final String[] lineFields = line.substring(2).split("="); if (lineFields.length == 2 && VCFHeaderVersion.isFormatString(lineFields[0]) ) { if ( !VCFHeaderVersion.isVersionString(lineFields[1]) ) throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version");
@Override public void setHeader(VCFHeader header) { VCFHeaderVersion version = null; // Normally AbstractVCFCodec parses the header and thereby sets the // version field. It gets used later on so we need to set it. for (final VCFHeaderLine line : header.getMetaDataInInputOrder()) { if (VCFHeaderVersion.isFormatString(line.getKey())) { version = VCFHeaderVersion.toHeaderVersion(line.getValue()); break; } } codec.setHeaderAndVersion(header, version); }
if (line.startsWith(VCFHeader.METADATA_INDICATOR)) { final String[] lineFields = line.substring(2).split("="); if (lineFields.length == 2 && VCFHeaderVersion.isFormatString(lineFields[0]) ) { if ( !VCFHeaderVersion.isVersionString(lineFields[1]) ) throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version");
if (line.startsWith(VCFHeader.METADATA_INDICATOR)) { final String[] lineFields = line.substring(2).split("="); if (lineFields.length == 2 && VCFHeaderVersion.isFormatString(lineFields[0]) ) { if ( !VCFHeaderVersion.isVersionString(lineFields[1]) ) throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version");
if (line.startsWith(VCFHeader.METADATA_INDICATOR)) { final String[] lineFields = line.substring(2).split("="); if (lineFields.length == 2 && VCFHeaderVersion.isFormatString(lineFields[0]) ) { if ( !VCFHeaderVersion.isVersionString(lineFields[1]) ) throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version");
if (line.startsWith(VCFHeader.METADATA_INDICATOR)) { final String[] lineFields = line.substring(2).split("="); if (lineFields.length == 2 && VCFHeaderVersion.isFormatString(lineFields[0]) ) { if ( !VCFHeaderVersion.isVersionString(lineFields[1]) ) throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version");
if (line.startsWith(VCFHeader.METADATA_INDICATOR)) { final String[] lineFields = line.substring(2).split("="); if (lineFields.length == 2 && VCFHeaderVersion.isFormatString(lineFields[0]) ) { if ( !VCFHeaderVersion.isVersionString(lineFields[1]) ) throw new TribbleException.InvalidHeader(lineFields[1] + " is not a supported version");