// validates aligned seq header.
private static void ValidateAlignedSequenceHeader(SAMAlignedSequenceHeader header)
{
string message = header.IsValid();
if (!string.IsNullOrEmpty(message))
{
throw new FormatException(message);
}
}
// Validates the alignment.
private SequenceAlignmentMap ValidateAlignment(ISequenceAlignment sequenceAlignment)
{
SequenceAlignmentMap seqAlignmentMap = sequenceAlignment as SequenceAlignmentMap;
if (seqAlignmentMap != null)
{
ValidateAlignmentHeader(seqAlignmentMap.Header);
if (CreateSortedBAMFile && SortType == BAMSortByFields.ChromosomeNameAndCoordinates)
{
this.refSequences = SortSequenceRanges(seqAlignmentMap.Header.GetReferenceSequenceRanges());
}
else
{
this.refSequences = seqAlignmentMap.Header.GetReferenceSequenceRanges();
}
return(seqAlignmentMap);
}
SAMAlignmentHeader header = sequenceAlignment.Metadata[Helper.SAMAlignmentHeaderKey] as SAMAlignmentHeader;
if (header == null)
{
throw new ArgumentException(Properties.Resource.SAMAlignmentHeaderNotFound);
}
ValidateAlignmentHeader(header);
seqAlignmentMap = new SequenceAlignmentMap(header);
if (CreateSortedBAMFile && SortType == BAMSortByFields.ChromosomeNameAndCoordinates)
{
this.refSequences = SortSequenceRanges(seqAlignmentMap.Header.GetReferenceSequenceRanges());
}
else
{
this.refSequences = seqAlignmentMap.Header.GetReferenceSequenceRanges();
}
foreach (IAlignedSequence alignedSeq in sequenceAlignment.AlignedSequences)
{
SAMAlignedSequenceHeader alignedHeader = alignedSeq.Metadata[Helper.SAMAlignedSequenceHeaderKey] as SAMAlignedSequenceHeader;
if (alignedHeader == null)
{
throw new ArgumentException(Properties.Resource.SAMAlignedSequenceHeaderNotFound);
}
SAMAlignedSequence samAlignedSeq = new SAMAlignedSequence(alignedHeader);
samAlignedSeq.QuerySequence = alignedSeq.Sequences[0];
seqAlignmentMap.QuerySequences.Add(samAlignedSeq);
}
return(seqAlignmentMap);
}
// Validates the alignment.
private SequenceAlignmentMap ValidateAlignment(ISequenceAlignment sequenceAlignment)
{
SequenceAlignmentMap seqAlignmentMap = sequenceAlignment as SequenceAlignmentMap;
if (seqAlignmentMap != null)
{
ValidateAlignmentHeader(seqAlignmentMap.Header);
_refSequences = SortSequenceRanges(seqAlignmentMap.Header.GetReferenceSequenceRanges());
foreach (SAMAlignedSequence alignedSequence in seqAlignmentMap.QuerySequences)
{
string message = alignedSequence.IsValidHeader();
if (!string.IsNullOrEmpty(message))
{
throw new ArgumentException(message);
}
ValidateSQHeader(alignedSequence.RName);
}
return(seqAlignmentMap);
}
SAMAlignmentHeader header = sequenceAlignment.Metadata[Helper.SAMAlignmentHeaderKey] as SAMAlignmentHeader;
if (header == null)
{
throw new ArgumentException(Resource.SAMAlignmentHeaderNotFound);
}
ValidateAlignmentHeader(header);
seqAlignmentMap = new SequenceAlignmentMap(header);
_refSequences = SortSequenceRanges(seqAlignmentMap.Header.GetReferenceSequenceRanges());
foreach (IAlignedSequence alignedSeq in sequenceAlignment.AlignedSequences)
{
SAMAlignedSequenceHeader alignedHeader = alignedSeq.Metadata[Helper.SAMAlignedSequenceHeaderKey] as SAMAlignedSequenceHeader;
if (alignedHeader == null)
{
throw new ArgumentException(Resource.SAMAlignedSequenceHeaderNotFound);
}
ValidateAlignedSequenceHeader(alignedHeader);
ValidateSQHeader(alignedHeader.RName);
SAMAlignedSequence samAlignedSeq = new SAMAlignedSequence(alignedHeader);
samAlignedSeq.QuerySequence = alignedSeq.Sequences[0];
}
return(seqAlignmentMap);
}
/// <summary>
/// Validate parser and formatter by parsing the same file which contains
/// extended CIGAR string. Validate the CIGAR property in aligned sequence
/// metadata information is updated as expected.
/// </summary>
/// <param name="nodeName">xml node name</param>
void ValidateSAMParseAndFormatWithCIGARFormat(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedSequenceFile = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string expectedCIGARString = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.CIGARNode);
// Create parser using encoding
ISequenceAlignmentParser parser = new SAMParser();
try
{
IList <ISequenceAlignment> alignments = parser.Parse(filePath);
// Get expected sequences
using (FastAParser parserObj = new FastAParser(expectedSequenceFile))
{
IEnumerable <ISequence> expectedSequences = parserObj.Parse();
IList <ISequence> expectedSequencesList = expectedSequences.ToList();
// Validate parsed output with expected output
int count = 0;
for (int index = 0; index < alignments.Count; index++)
{
for (int ialigned = 0; ialigned <
alignments[index].AlignedSequences.Count; ialigned++)
{
for (int iseq = 0; iseq <
alignments[index].AlignedSequences[ialigned].Sequences.Count; iseq++)
{
Assert.AreEqual(new string(expectedSequencesList[count].Select(a => (char)a).ToArray()),
new string(alignments[index].AlignedSequences[ialigned].Sequences[iseq].Select(a => (char)a).ToArray()));
foreach (string key in alignments[index].AlignedSequences[ialigned].Metadata.Keys)
{
SAMAlignedSequenceHeader header = (SAMAlignedSequenceHeader)
alignments[index].AlignedSequences[ialigned].Metadata[key];
Assert.AreEqual(expectedCIGARString, header.CIGAR);
}
count++;
}
}
}
}
}
finally
{
(parser as SAMParser).Dispose();
}
}
/// <summary>
/// Validate parser and formatter by parsing the same file which contains
/// extended CIGAR string. Validate the CIGAR property in aligned sequence
/// metadata information is updated as expected.
/// </summary>
/// <param name="nodeName">xml node name</param>
void ValidateSAMParseAndFormatWithCIGARFormat(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = Utility._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedSequenceFile = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string expectedCIGARString = Utility._xmlUtil.GetTextValue(
nodeName, Constants.CIGARNode);
// Create parser using encoding
ISequenceAlignmentParser parser = new SAMParser();
IList <ISequenceAlignment> alignments = parser.Parse(filePath);
// Get expected sequences
FastaParser parserObj = new FastaParser();
IList <ISequence> expectedSequences = parserObj.Parse(expectedSequenceFile);
// Validate parsed output with expected output
int count = 0;
for (int index = 0; index < alignments.Count; index++)
{
for (int ialigned = 0; ialigned <
alignments[index].AlignedSequences.Count; ialigned++)
{
for (int iseq = 0; iseq <
alignments[index].AlignedSequences[ialigned].Sequences.Count; iseq++)
{
Assert.AreEqual(expectedSequences[count].ToString(),
alignments[index].AlignedSequences[ialigned].Sequences[iseq].ToString());
foreach (string key in alignments[index].AlignedSequences[ialigned].Metadata.Keys)
{
SAMAlignedSequenceHeader header = (SAMAlignedSequenceHeader)
alignments[index].AlignedSequences[ialigned].Metadata[key];
Assert.AreEqual(expectedCIGARString, header.CIGAR.ToString());
}
count++;
}
}
}
}
// Validates the alignment.
private SequenceAlignmentMap ValidateAlignment(ISequenceAlignment sequenceAlignment)
{
SequenceAlignmentMap seqAlignmentMap = sequenceAlignment as SequenceAlignmentMap;
if (seqAlignmentMap != null)
{
ValidateAlignmentHeader(seqAlignmentMap.Header);
_refSequences = SortSequenceRanges(seqAlignmentMap.Header.GetReferenceSequenceRanges());
return(seqAlignmentMap);
}
SAMAlignmentHeader header = sequenceAlignment.Metadata[Helper.SAMAlignmentHeaderKey] as SAMAlignmentHeader;
if (header == null)
{
throw new ArgumentException(Resource.SAMAlignmentHeaderNotFound);
}
ValidateAlignmentHeader(header);
seqAlignmentMap = new SequenceAlignmentMap(header);
_refSequences = SortSequenceRanges(seqAlignmentMap.Header.GetReferenceSequenceRanges());
foreach (IAlignedSequence alignedSeq in sequenceAlignment.AlignedSequences)
{
SAMAlignedSequenceHeader alignedHeader = alignedSeq.Metadata[Helper.SAMAlignedSequenceHeaderKey] as SAMAlignedSequenceHeader;
if (alignedHeader == null)
{
throw new ArgumentException(Resource.SAMAlignedSequenceHeaderNotFound);
}
SAMAlignedSequence samAlignedSeq = new SAMAlignedSequence(alignedHeader);
samAlignedSeq.QuerySequence = alignedSeq.Sequences[0];
seqAlignmentMap.QuerySequences.Add(samAlignedSeq);
}
return(seqAlignmentMap);
}
