//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Requires({"name != null", "! ( location == null && output == null )", "! ( enableOnTheFlyIndexing && location == null )"}) protected IndexingVariantContextWriter(final String name, final File location, final OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict, final boolean enableOnTheFlyIndexing)
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
protected internal IndexingVariantContextWriter(string name, File location, OutputStream output, SAMSequenceDictionary refDict, bool enableOnTheFlyIndexing)
{
outputStream = output;
this.name = name;
this.refDict = refDict;
if (enableOnTheFlyIndexing)
{
try
{
idxStream = new LittleEndianOutputStream(new FileOutputStream(Tribble.indexFile(location)));
//System.out.println("Creating index on the fly for " + location);
indexer = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
indexer.initialize(location, indexer.defaultBinSize());
positionalOutputStream = new PositionalOutputStream(output);
outputStream = positionalOutputStream;
}
catch (IOException ex)
{
// No matter what we keep going, since we don't care if we can't create the index file
idxStream = null;
indexer = null;
positionalOutputStream = null;
}
}
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public VCFWriter(final File location, final OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict, final boolean enableOnTheFlyIndexing, boolean doNotWriteGenotypes, final boolean allowMissingFieldsInHeader)
public VCFWriter(File location, OutputStream output, SAMSequenceDictionary refDict, bool enableOnTheFlyIndexing, bool doNotWriteGenotypes, bool allowMissingFieldsInHeader) : base(writerName(location, output), location, output, refDict, enableOnTheFlyIndexing)
{
this.doNotWriteGenotypes = doNotWriteGenotypes;
this.allowMissingFieldsInHeader = allowMissingFieldsInHeader;
this.charset = Charset.forName("ISO-8859-1");
this.writer = new OutputStreamWriter(lineBuffer, charset);
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public VCFWriter(final File location, final OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict, final boolean enableOnTheFlyIndexing, boolean doNotWriteGenotypes, final boolean allowMissingFieldsInHeader)
public VCFWriter(File location, OutputStream output, SAMSequenceDictionary refDict, bool enableOnTheFlyIndexing, bool doNotWriteGenotypes, bool allowMissingFieldsInHeader) : base(writerName(location, output), location, output, refDict, enableOnTheFlyIndexing)
{
this.doNotWriteGenotypes = doNotWriteGenotypes;
this.allowMissingFieldsInHeader = allowMissingFieldsInHeader;
this.charset = Charset.forName("ISO-8859-1");
this.writer = new OutputStreamWriter(lineBuffer, charset);
}
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Requires({"name != null", "! ( location == null && output == null )", "! ( enableOnTheFlyIndexing && location == null )"}) protected IndexingVariantContextWriter(final String name, final File location, final OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict, final boolean enableOnTheFlyIndexing)
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
protected internal IndexingVariantContextWriter(string name, File location, OutputStream output, SAMSequenceDictionary refDict, bool enableOnTheFlyIndexing)
{
outputStream = output;
this.name = name;
this.refDict = refDict;
if (enableOnTheFlyIndexing)
{
try
{
idxStream = new LittleEndianOutputStream(new FileOutputStream(Tribble.indexFile(location)));
//System.out.println("Creating index on the fly for " + location);
indexer = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
indexer.initialize(location, indexer.defaultBinSize());
positionalOutputStream = new PositionalOutputStream(output);
outputStream = positionalOutputStream;
}
catch (IOException ex)
{
// No matter what we keep going, since we don't care if we can't create the index file
idxStream = null;
indexer = null;
positionalOutputStream = null;
}
}
}
private static void setIndexSequenceDictionary(Index index, SAMSequenceDictionary dict)
{
foreach (SAMSequenceRecord seq in dict.Sequences)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final String contig = SequenceDictionaryPropertyPredicate + seq.getSequenceName();
string contig = SequenceDictionaryPropertyPredicate + seq.SequenceName;
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final String length = String.valueOf(seq.getSequenceLength());
string length = Convert.ToString(seq.SequenceLength);
index.addProperty(contig, length);
}
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VariantContextWriter create(final java.io.File location, final java.io.OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict, final java.util.EnumSet<Options> options)
public static VariantContextWriter create(File location, OutputStream output, SAMSequenceDictionary refDict, EnumSet<Options> options)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final boolean enableBCF = isBCFOutput(location, options);
bool enableBCF = isBCFOutput(location, options);
if (enableBCF)
{
return new BCF2Writer(location, output, refDict, options.contains(Options.INDEX_ON_THE_FLY), options.contains(Options.DO_NOT_WRITE_GENOTYPES));
}
else
{
return new VCFWriter(location, output, refDict, options.contains(Options.INDEX_ON_THE_FLY), options.contains(Options.DO_NOT_WRITE_GENOTYPES), options.contains(Options.ALLOW_MISSING_FIELDS_IN_HEADER));
}
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public BCF2Writer(final File location, final OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict, final boolean enableOnTheFlyIndexing, final boolean doNotWriteGenotypes)
public BCF2Writer(File location, OutputStream output, SAMSequenceDictionary refDict, bool enableOnTheFlyIndexing, bool doNotWriteGenotypes) : base(writerName(location, output), location, output, refDict, enableOnTheFlyIndexing)
{
this.outputStream = OutputStream;
this.doNotWriteGenotypes = doNotWriteGenotypes;
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VariantContextWriter create(final java.io.File location, final java.io.OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict, final java.util.EnumSet<Options> options)
public static VariantContextWriter create(File location, OutputStream output, SAMSequenceDictionary refDict, EnumSet <Options> options)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final boolean enableBCF = isBCFOutput(location, options);
bool enableBCF = isBCFOutput(location, options);
if (enableBCF)
{
return(new BCF2Writer(location, output, refDict, options.contains(Options.INDEX_ON_THE_FLY), options.contains(Options.DO_NOT_WRITE_GENOTYPES)));
}
else
{
return(new VCFWriter(location, output, refDict, options.contains(Options.INDEX_ON_THE_FLY), options.contains(Options.DO_NOT_WRITE_GENOTYPES), options.contains(Options.ALLOW_MISSING_FIELDS_IN_HEADER)));
}
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VariantContextWriter create(final java.io.OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict, final java.util.EnumSet<Options> options)
public static VariantContextWriter create(OutputStream output, SAMSequenceDictionary refDict, EnumSet <Options> options)
{
return(create(null, output, refDict, options));
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VariantContextWriter create(final java.io.File location, final java.io.OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict)
public static VariantContextWriter create(File location, OutputStream output, SAMSequenceDictionary refDict)
{
return(create(location, output, refDict, DEFAULT_OPTIONS));
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VariantContextWriter create(final java.io.File location, final net.sf.samtools.SAMSequenceDictionary refDict, final java.util.EnumSet<Options> options)
public static VariantContextWriter create(File location, SAMSequenceDictionary refDict, EnumSet <Options> options)
{
return(create(location, openOutputStream(location), refDict, options));
}
private static void setIndexSequenceDictionary(Index index, SAMSequenceDictionary dict)
{
foreach (SAMSequenceRecord seq in dict.Sequences)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final String contig = SequenceDictionaryPropertyPredicate + seq.getSequenceName();
string contig = SequenceDictionaryPropertyPredicate + seq.SequenceName;
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final String length = String.valueOf(seq.getSequenceLength());
string length = Convert.ToString(seq.SequenceLength);
index.addProperty(contig,length);
}
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VariantContextWriter create(final java.io.OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict, final java.util.EnumSet<Options> options)
public static VariantContextWriter create(OutputStream output, SAMSequenceDictionary refDict, EnumSet<Options> options)
{
return create(null, output, refDict, options);
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VariantContextWriter create(final java.io.File location, final java.io.OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict)
public static VariantContextWriter create(File location, OutputStream output, SAMSequenceDictionary refDict)
{
return create(location, output, refDict, DEFAULT_OPTIONS);
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VariantContextWriter create(final java.io.File location, final net.sf.samtools.SAMSequenceDictionary refDict, final java.util.EnumSet<Options> options)
public static VariantContextWriter create(File location, SAMSequenceDictionary refDict, EnumSet<Options> options)
{
return create(location, openOutputStream(location), refDict, options);
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public BCF2Writer(final File location, final OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict, final boolean enableOnTheFlyIndexing, final boolean doNotWriteGenotypes)
public BCF2Writer(File location, OutputStream output, SAMSequenceDictionary refDict, bool enableOnTheFlyIndexing, bool doNotWriteGenotypes) : base(writerName(location, output), location, output, refDict, enableOnTheFlyIndexing)
{
this.outputStream = OutputStream;
this.doNotWriteGenotypes = doNotWriteGenotypes;
}
