/// <summary>
/// Writes specified SAMAlignedHeader to specified text writer.
/// </summary>
/// <param name="header">Header to write.</param>
/// <param name="writer">Text writer.</param>
public static void WriteHeader(SAMAlignmentHeader header, TextWriter writer)
{
if (header == null)
{
return;
}
if (writer == null)
{
throw new ArgumentNullException("writer");
}
string message = header.IsValid();
if (!string.IsNullOrEmpty(message))
{
throw new ArgumentException(message);
}
StringBuilder headerLine = null;
for (int i = 0; i < header.RecordFields.Count; i++)
{
headerLine = new StringBuilder();
headerLine.Append("@");
headerLine.Append(header.RecordFields[i].Typecode);
for (int j = 0; j < header.RecordFields[i].Tags.Count; j++)
{
headerLine.Append("\t");
headerLine.Append(header.RecordFields[i].Tags[j].Tag);
headerLine.Append(":");
headerLine.Append(header.RecordFields[i].Tags[j].Value);
}
writer.WriteLine(headerLine.ToString());
}
foreach (string comment in header.Comments)
{
headerLine = new StringBuilder();
headerLine.Append("@CO");
headerLine.Append("\t");
headerLine.Append(comment);
writer.WriteLine(headerLine.ToString());
}
writer.Flush();
}
private static SAMAlignmentHeader ParseSamHeader(List <string> headerStrings)
{
SAMAlignmentHeader samHeader = new SAMAlignmentHeader();
foreach (string headerString in headerStrings)
{
string[] tokens = headerString.Split(tabDelim, StringSplitOptions.RemoveEmptyEntries);
string recordTypecode = tokens[0].Substring(1);
// Validate the header format.
ValidateHeaderLineFormat(headerString);
SAMRecordField headerLine = null;
if (string.Compare(recordTypecode, "CO", StringComparison.OrdinalIgnoreCase) != 0)
{
List <string> tags = new List <string>();
headerLine = new SAMRecordField(recordTypecode);
for (int i = 1; i < tokens.Length; i++)
{
string tagToken = tokens[i];
string tagName = tagToken.Substring(0, 2);
tags.Add(tagName);
headerLine.Tags.Add(new SAMRecordFieldTag(tagName, tagToken.Substring(3)));
}
samHeader.RecordFields.Add(headerLine);
}
else
{
samHeader.Comments.Add(headerString.Substring(4));
}
}
IList <ReferenceSequenceInfo> referenceSeqsInfo = samHeader.GetReferenceSequencesInfoFromSQHeader();
foreach (var item in referenceSeqsInfo)
{
samHeader.ReferenceSequences.Add(item);
}
string message = samHeader.IsValid();
if (!string.IsNullOrEmpty(message))
{
throw new FormatException(message);
}
return(samHeader);
}
/// <summary>
/// Writes specified SAMAlignedHeader to specified text writer.
/// </summary>
/// <param name="writer">Text Writer</param>
/// <param name="header">Header to write.</param>
public static void WriteHeader(TextWriter writer, SAMAlignmentHeader header)
{
if (header == null)
{
return;
}
if (writer == null)
{
throw new ArgumentNullException("writer");
}
string message = header.IsValid();
if (!string.IsNullOrEmpty(message))
{
throw new ArgumentException(message);
}
StringBuilder headerLine = null;
foreach (SAMRecordField record in header.RecordFields)
{
headerLine = new StringBuilder();
headerLine.Append("@");
headerLine.Append(record.Typecode);
foreach (SAMRecordFieldTag tag in record.Tags)
{
headerLine.Append("\t");
headerLine.Append(tag.Tag);
headerLine.Append(":");
headerLine.Append(tag.Value);
}
writer.WriteLine(headerLine.ToString());
}
foreach (string comment in header.Comments)
{
headerLine = new StringBuilder();
headerLine.Append("@CO");
headerLine.Append("\t");
headerLine.Append(comment);
writer.WriteLine(headerLine.ToString());
}
writer.Flush();
}
/// <summary>
/// Parses SAM alignment header from specified BioTextReader.
/// </summary>
/// <param name="bioReader">Bio text reader.</param>
private static SAMAlignmentHeader ParserSAMHeader(BioTextReader bioReader)
{
SAMAlignmentHeader samHeader = new SAMAlignmentHeader();
if (bioReader.HasLines && bioReader.Line.StartsWith(@"@", StringComparison.OrdinalIgnoreCase))
{
while (bioReader.HasLines && bioReader.Line.StartsWith(@"@", StringComparison.OrdinalIgnoreCase))
{
string[] tokens = bioReader.Line.Split(tabDelim, StringSplitOptions.RemoveEmptyEntries);
string recordTypecode = tokens[0].Substring(1);
// Validate the header format.
ValidateHeaderLineFormat(bioReader.Line);
SAMRecordField headerLine = null;
if (string.Compare(recordTypecode, "CO", StringComparison.OrdinalIgnoreCase) != 0)
{
List <string> tags = new List <string>();
headerLine = new SAMRecordField(recordTypecode);
for (int i = 1; i < tokens.Length; i++)
{
string tagToken = tokens[i];
string tagName = tagToken.Substring(0, 2);
tags.Add(tagName);
headerLine.Tags.Add(new SAMRecordFieldTag(tagName, tagToken.Substring(3)));
}
samHeader.RecordFields.Add(headerLine);
}
else
{
samHeader.Comments.Add(bioReader.Line.Substring(4));
}
bioReader.GoToNextLine();
}
string message = samHeader.IsValid();
if (!string.IsNullOrEmpty(message))
{
throw new FormatException(message);
}
}
return(samHeader);
}
// Validates alignment header.
private static void ValidateAlignmentHeader(SAMAlignmentHeader header)
{
string message = header.IsValid();
if (!string.IsNullOrEmpty(message))
{
throw new ArgumentException(message);
}
}
/// <summary>
/// Writes specified SAMAlignedHeader to specified text writer.
/// </summary>
/// <param name="writer">Text Writer</param>
/// <param name="header">Header to write.</param>
public static void WriteHeader(TextWriter writer, SAMAlignmentHeader header)
{
if (header == null)
{
return;
}
if (writer == null)
{
throw new ArgumentNullException("writer");
}
string message = header.IsValid();
if (!string.IsNullOrEmpty(message))
{
throw new ArgumentException(message);
}
StringBuilder headerLine = null;
foreach (SAMRecordField record in header.RecordFields)
{
headerLine = new StringBuilder();
headerLine.Append("@");
headerLine.Append(record.Typecode);
foreach (SAMRecordFieldTag tag in record.Tags)
{
headerLine.Append("\t");
headerLine.Append(tag.Tag);
headerLine.Append(":");
headerLine.Append(tag.Value);
}
writer.WriteLine(headerLine.ToString());
}
foreach (string comment in header.Comments)
{
headerLine = new StringBuilder();
headerLine.Append("@CO");
headerLine.Append("\t");
headerLine.Append(comment);
writer.WriteLine(headerLine.ToString());
}
writer.Flush();
}