/// <summary>
/// General method to Invalidate Quality Sequences
/// <param name="method">enum type to execute different overload</param>
/// </summary>
private static void ValidateQualitySeqLength(ParseOrFormatQualLength method)
{
SAMAlignedSequence align = new SAMAlignedSequence();
try
{
switch (method)
{
case ParseOrFormatQualLength.AlignedSeq:
SAMParser.ParseQualityNSequence(
align,
Alphabets.DNA,
null,
String.Empty);
break;
case ParseOrFormatQualLength.Sequencedata:
align.QName = "Quality Value";
SAMParser.ParseQualityNSequence(
align,
Alphabets.DNA,
null,
String.Empty);
break;
case ParseOrFormatQualLength.Qualitydata:
align.QName = "Quality Value";
SAMParser.ParseQualityNSequence(
align,
Alphabets.DNA,
null,
Constants.QualitySequence);
break;
case ParseOrFormatQualLength.QualityLength:
align.QName = "Quality Value";
SAMParser.ParseQualityNSequence(
align,
Alphabets.DNA,
null,
Constants.QualitySequence);
break;
default:
break;
}
Assert.Fail();
}
catch (ArgumentException)
{
ApplicationLog.WriteLine(
"SAM Parser P2 : Successfully validated the exception");
}
catch (FormatException)
{
ApplicationLog.WriteLine(
"SAM Parser P2 : Successfully validated the exception");
}
}
/// <summary>
/// Returns an aligned sequence by parses the BAM file.
/// </summary>
private SAMAlignedSequence GetAlignedSequence(int start, int end)
{
byte[] array = new byte[4];
ReadUnCompressedData(array, 0, 4);
int blockLen = Helper.GetInt32(array, 0);
byte[] alignmentBlock = new byte[blockLen];
ReadUnCompressedData(alignmentBlock, 0, blockLen);
SAMAlignedSequence alignedSeq = new SAMAlignedSequence();
int value;
UInt32 UnsignedValue;
// 0-4 bytes
int refSeqIndex = Helper.GetInt32(alignmentBlock, 0);
if (refSeqIndex == -1)
{
alignedSeq.RName = "*";
}
else
{
alignedSeq.RName = refSeqNames[refSeqIndex];
}
// 4-8 bytes
alignedSeq.Pos = Helper.GetInt32(alignmentBlock, 4) + 1;
// if there is no overlap no need to parse further.
// BAMPos > closedEnd
// => (alignedSeq.Pos - 1) > end -1
if (alignedSeq.Pos > end)
{
return(null);
}
// 8 - 12 bytes "bin<<16|mapQual<<8|read_name_len"
UnsignedValue = Helper.GetUInt32(alignmentBlock, 8);
// 10 -12 bytes
alignedSeq.Bin = (int)(UnsignedValue & 0xFFFF0000) >> 16;
// 9th bytes
alignedSeq.MapQ = (int)(UnsignedValue & 0x0000FF00) >> 8;
// 8th bytes
int queryNameLen = (int)(UnsignedValue & 0x000000FF);
// 12 - 16 bytes
UnsignedValue = Helper.GetUInt32(alignmentBlock, 12);
// 14-16 bytes
int flagValue = (int)(UnsignedValue & 0xFFFF0000) >> 16;
alignedSeq.Flag = (SAMFlags)flagValue;
// 12-14 bytes
int cigarLen = (int)(UnsignedValue & 0x0000FFFF);
// 16-20 bytes
int readLen = Helper.GetInt32(alignmentBlock, 16);
// 20-24 bytes
int mateRefSeqIndex = Helper.GetInt32(alignmentBlock, 20);
if (mateRefSeqIndex != -1)
{
alignedSeq.MRNM = refSeqNames[mateRefSeqIndex];
}
else
{
alignedSeq.MRNM = "*";
}
// 24-28 bytes
alignedSeq.MPos = Helper.GetInt32(alignmentBlock, 24) + 1;
// 28-32 bytes
alignedSeq.ISize = Helper.GetInt32(alignmentBlock, 28);
// 32-(32+readLen) bytes
alignedSeq.QName = System.Text.ASCIIEncoding.ASCII.GetString(alignmentBlock, 32, queryNameLen - 1);
StringBuilder strbuilder = new StringBuilder();
int startIndex = 32 + queryNameLen;
for (int i = startIndex; i < (startIndex + cigarLen * 4); i += 4)
{
// Get the CIGAR operation length stored in first 28 bits.
UInt32 cigarValue = Helper.GetUInt32(alignmentBlock, i);
strbuilder.Append(((cigarValue & 0xFFFFFFF0) >> 4).ToString(CultureInfo.InvariantCulture));
// Get the CIGAR operation stored in last 4 bits.
value = (int)cigarValue & 0x0000000F;
// MIDNSHP=>0123456
switch (value)
{
case 0:
strbuilder.Append("M");
break;
case 1:
strbuilder.Append("I");
break;
case 2:
strbuilder.Append("D");
break;
case 3:
strbuilder.Append("N");
break;
case 4:
strbuilder.Append("S");
break;
case 5:
strbuilder.Append("H");
break;
case 6:
strbuilder.Append("P");
break;
case 7:
strbuilder.Append("=");
break;
case 8:
strbuilder.Append("X");
break;
default:
throw new FileFormatException(Properties.Resource.BAM_InvalidCIGAR);
}
}
string cigar = strbuilder.ToString();
if (string.IsNullOrWhiteSpace(cigar))
{
alignedSeq.CIGAR = "*";
}
else
{
alignedSeq.CIGAR = cigar;
}
// if there is no overlap no need to parse further.
// ZeroBasedRefEnd < start
// => (alignedSeq.RefEndPos -1) < start
if (alignedSeq.RefEndPos - 1 < start && alignedSeq.RName != Properties.Resource.SAM_NO_REFERENCE_DEFINED_INDICATOR)
{
return(null);
}
startIndex += cigarLen * 4;
strbuilder = new StringBuilder();
int index = startIndex;
for (; index < (startIndex + (readLen + 1) / 2) - 1; index++)
{
// Get first 4 bit value
value = (alignmentBlock[index] & 0xF0) >> 4;
strbuilder.Append(GetSeqChar(value));
// Get last 4 bit value
value = alignmentBlock[index] & 0x0F;
strbuilder.Append(GetSeqChar(value));
}
value = (alignmentBlock[index] & 0xF0) >> 4;
strbuilder.Append(GetSeqChar(value));
if (readLen % 2 == 0)
{
value = alignmentBlock[index] & 0x0F;
strbuilder.Append(GetSeqChar(value));
}
startIndex = index + 1;
string strSequence = strbuilder.ToString();
byte[] qualValues = new byte[readLen];
string strQualValues = "*";
if (alignmentBlock[startIndex] != 0xFF)
{
for (int i = startIndex; i < (startIndex + readLen); i++)
{
qualValues[i - startIndex] = (byte)(alignmentBlock[i] + 33);
}
strQualValues = System.Text.ASCIIEncoding.ASCII.GetString(qualValues);
}
SAMParser.ParseQualityNSequence(alignedSeq, Alphabet, strSequence, strQualValues);
startIndex += readLen;
if (alignmentBlock.Length > startIndex + 4 && alignmentBlock[startIndex] != 0x0 && alignmentBlock[startIndex + 1] != 0x0)
{
for (index = startIndex; index < alignmentBlock.Length;)
{
SAMOptionalField optionalField = new SAMOptionalField();
optionalField.Tag = System.Text.ASCIIEncoding.ASCII.GetString(alignmentBlock, index, 2);
index += 2;
char vType = (char)alignmentBlock[index++];
string valueType = vType.ToString();
// SAM format supports [AifZH] for value type.
// In BAM, an integer may be stored as a signed 8-bit integer (c), unsigned 8-bit integer (C), signed short (s), unsigned
// short (S), signed 32-bit (i) or unsigned 32-bit integer (I), depending on the signed magnitude of the integer. However,
// in SAM, all types of integers are presented as type ʻiʼ.
string message = Helper.IsValidPatternValue("VType", valueType, BAMOptionalFieldRegex);
if (!string.IsNullOrEmpty(message))
{
throw new FormatException(message);
}
optionalField.Value = GetOptionalValue(vType, alignmentBlock, ref index).ToString();
// Convert to SAM format.
if ("cCsSI".IndexOf(vType) >= 0)
{
valueType = "i";
}
optionalField.VType = valueType;
alignedSeq.OptionalFields.Add(optionalField);
}
}
return(alignedSeq);
}
protected override SAMAlignedSequence GetAlignedSequence()
{
byte[] array = new byte[4];
ReadUnCompressedData(array, 0, 4);
int blockLen = Helper.GetInt32(array, 0);
byte[] alignmentBlock = new byte[blockLen];
ReadUnCompressedData(alignmentBlock, 0, blockLen);
if (!Filter.Accept(alignmentBlock))
{
return(null);
}
SAMAlignedSequence alignedSeq = new SAMAlignedSequence();
int value;
UInt32 UnsignedValue;
// 0-4 bytes
int refSeqIndex = Helper.GetInt32(alignmentBlock, 0);
if (refSeqIndex == -1)
{
alignedSeq.SetPreValidatedRName("*");
}
else
{
alignedSeq.SetPreValidatedRName(RefSeqNames[refSeqIndex]);
}
// 4-8 bytes
alignedSeq.Pos = Helper.GetInt32(alignmentBlock, 4) + 1;
// 8 - 12 bytes "bin<<16|mapQual<<8|read_name_len"
UnsignedValue = Helper.GetUInt32(alignmentBlock, 8);
// 10 -12 bytes
//alignedSeq.Bin = (int)(UnsignedValue & 0xFFFF0000) >> 16;
// 9th bytes
alignedSeq.MapQ = (int)(UnsignedValue & 0x0000FF00) >> 8;
// 8th bytes
int queryNameLen = (int)(UnsignedValue & 0x000000FF);
// 12 - 16 bytes
UnsignedValue = Helper.GetUInt32(alignmentBlock, 12);
// 14-16 bytes
int flagValue = (int)(UnsignedValue & 0xFFFF0000) >> 16;
alignedSeq.Flag = (SAMFlags)flagValue;
// 12-14 bytes
int cigarLen = (int)(UnsignedValue & 0x0000FFFF);
// 16-20 bytes
int readLen = Helper.GetInt32(alignmentBlock, 16);
// 20-24 bytes
int mateRefSeqIndex = Helper.GetInt32(alignmentBlock, 20);
if (mateRefSeqIndex != -1)
{
alignedSeq.SetPreValidatedMRNM(RefSeqNames[mateRefSeqIndex]);
}
else
{
alignedSeq.SetPreValidatedMRNM("*");
}
// 24-28 bytes
alignedSeq.MPos = Helper.GetInt32(alignmentBlock, 24) + 1;
// 28-32 bytes
alignedSeq.ISize = Helper.GetInt32(alignmentBlock, 28);
// 32-(32+readLen) bytes
alignedSeq.QName = System.Text.ASCIIEncoding.ASCII.GetString(alignmentBlock, 32, queryNameLen - 1);
StringBuilder strbuilder = new StringBuilder();
int startIndex = 32 + queryNameLen;
for (int i = startIndex; i < (startIndex + cigarLen * 4); i += 4)
{
// Get the CIGAR operation length stored in first 28 bits.
UInt32 cigarValue = Helper.GetUInt32(alignmentBlock, i);
strbuilder.Append(((cigarValue & 0xFFFFFFF0) >> 4).ToString(CultureInfo.InvariantCulture));
// Get the CIGAR operation stored in last 4 bits.
value = (int)cigarValue & 0x0000000F;
// MIDNSHP=>0123456
switch (value)
{
case 0:
strbuilder.Append("M");
break;
case 1:
strbuilder.Append("I");
break;
case 2:
strbuilder.Append("D");
break;
case 3:
strbuilder.Append("N");
break;
case 4:
strbuilder.Append("S");
break;
case 5:
strbuilder.Append("H");
break;
case 6:
strbuilder.Append("P");
break;
case 7:
strbuilder.Append("=");
break;
case 8:
strbuilder.Append("X");
break;
default:
throw new Exception("Invalid CIGAR of query " + alignedSeq.QName);
}
}
string cigar = strbuilder.ToString();
if (string.IsNullOrWhiteSpace(cigar))
{
alignedSeq.SetPreValidatedCIGAR("*");
}
else
{
alignedSeq.SetPreValidatedCIGAR(cigar);
}
startIndex += cigarLen * 4;
var sequence = new byte[readLen];
int sequenceIndex = 0;
int index = startIndex;
for (; index < (startIndex + (readLen + 1) / 2) - 1; index++)
{
// Get first 4 bit value
value = (alignmentBlock[index] & 0xF0) >> 4;
sequence[sequenceIndex++] = GetSeqCharAsByte(value);
// Get last 4 bit value
value = alignmentBlock[index] & 0x0F;
sequence[sequenceIndex++] = GetSeqCharAsByte(value);
}
value = (alignmentBlock[index] & 0xF0) >> 4;
sequence[sequenceIndex++] = GetSeqCharAsByte(value);
if (readLen % 2 == 0)
{
value = alignmentBlock[index] & 0x0F;
sequence[sequenceIndex++] = GetSeqCharAsByte(value);
}
startIndex = index + 1;
byte[] qualValues = new byte[readLen];
if (alignmentBlock[startIndex] != 0xFF)
{
for (int i = startIndex; i < (startIndex + readLen); i++)
{
qualValues[i - startIndex] = (byte)(alignmentBlock[i] + 33);
}
//validate quality scores here
byte badVal;
bool ok = QualitativeSequence.ValidateQualScores(qualValues, SAMParser.QualityFormatType, out badVal);
if (!ok)
{
string message = string.Format("Invalid encoded quality score found: {0}", (char)badVal);
throw new ArgumentOutOfRangeException("encodedQualityScores", message);
}
}
else
{
qualValues = new byte[] { SAMParser.AsteriskAsByte };
}
//Values have already been validated when first parsed at this point so no need to again
SAMParser.ParseQualityNSequence(alignedSeq, Alphabet, sequence, qualValues, false);
startIndex += readLen;
if (alignmentBlock.Length > startIndex + 4 && alignmentBlock[startIndex] != 0x0 && alignmentBlock[startIndex + 1] != 0x0)
{
for (index = startIndex; index < alignmentBlock.Length;)
{
SAMOptionalField optionalField = new SAMOptionalField();
optionalField.Tag = System.Text.ASCIIEncoding.ASCII.GetString(alignmentBlock, index, 2);
index += 2;
char vType = (char)alignmentBlock[index++];
// SAM format supports [AifZH] for value type.
// In BAM, an integer may be stored as a signed 8-bit integer (c), unsigned 8-bit integer (C), signed short (s), unsigned
// short (S), signed 32-bit (i) or unsigned 32-bit integer (I), depending on the signed magnitude of the integer. However,
// in SAM, all types of integers are presented as type ʻiʼ.
//NOTE: Code previously here checked for valid value and threw an exception here, but this exception/validation is checked for in this method below, as while as when the value is set.
optionalField.Value = GetOptionalValue(vType, alignmentBlock, ref index).ToString();
// Convert to SAM format, where all integers are represented the same way
if ("cCsSI".IndexOf(vType) >= 0)
{
vType = 'i';
}
optionalField.VType = vType.ToString();
alignedSeq.OptionalFields.Add(optionalField);
}
}
return(alignedSeq);
}
