public void TestFormatter()
{
string filePath = @"TestUtils\BAM\SeqAlignment.bam";
string outputfilePath = "BAMTests123.bam";
BAMParser parser = null;
try
{
parser = new BAMParser();
BAMFormatter formatter = new BAMFormatter();
SequenceAlignmentMap alignmentMap = parser.Parse(filePath);
Assert.IsTrue(alignmentMap != null);
Assert.AreEqual(alignmentMap.Header.GetReferenceSequencesInfoFromSQHeader().Count, 1);
Assert.AreEqual(alignmentMap.Header.ReferenceSequences.Count, 1);
Assert.AreEqual(alignmentMap.QuerySequences.Count, 2);
formatter.Format(alignmentMap, outputfilePath);
formatter.CreateSortedBAMFile = true;
formatter.CreateIndexFile = true;
alignmentMap = parser.Parse(filePath);
formatter.Format(alignmentMap, outputfilePath);
Assert.IsTrue(File.Exists("BAMTests123.bam.bai"));
alignmentMap = parser.Parse(outputfilePath);
Assert.IsTrue(alignmentMap != null);
Assert.AreEqual(alignmentMap.Header.GetReferenceSequencesInfoFromSQHeader().Count, 1);
Assert.AreEqual(alignmentMap.Header.ReferenceSequences.Count, 1);
Assert.AreEqual(alignmentMap.QuerySequences.Count, 2);
alignmentMap = parser.ParseRange("BAMTests123.bam", new SequenceRange("chr20", 0, int.MaxValue));
Assert.IsTrue(alignmentMap != null);
Assert.AreEqual(alignmentMap.Header.GetReferenceSequencesInfoFromSQHeader().Count, 1);
Assert.AreEqual(alignmentMap.Header.ReferenceSequences.Count, 1);
Assert.AreEqual(alignmentMap.QuerySequences.Count, 2);
alignmentMap = parser.ParseRange("BAMTests123.bam", new SequenceRange("chr20", 0, 28833));
Assert.IsTrue(alignmentMap != null);
Assert.AreEqual(alignmentMap.Header.GetReferenceSequencesInfoFromSQHeader().Count, 1);
Assert.AreEqual(alignmentMap.Header.ReferenceSequences.Count, 1);
Assert.AreEqual(alignmentMap.QuerySequences.Count, 1);
}
finally
{
if (parser != null)
{
parser.Dispose();
}
}
}
public void TestFormatter()
{
string filePath = @"TestUtils\BAM\SeqAlignment.bam".TestDir();
const string outputfilePath = "BAMTests123.bam";
string outputIndexFile = outputfilePath + ".bai";
BAMParser parser = new BAMParser();
SequenceAlignmentMap alignmentMap = parser.ParseOne <SequenceAlignmentMap>(filePath);
Assert.IsNotNull(alignmentMap);
Assert.IsNotNull(alignmentMap.Header);
Assert.AreEqual(alignmentMap.Header.GetReferenceSequencesInfoFromSQHeader().Count, 1);
Assert.AreEqual(alignmentMap.Header.ReferenceSequences.Count, 1);
Assert.IsNotNull(alignmentMap.QuerySequences);
Assert.AreEqual(alignmentMap.QuerySequences.Count, 2);
BAMFormatter formatter = new BAMFormatter();
formatter.Format(alignmentMap, outputfilePath);
formatter.CreateSortedBAMFile = true;
formatter.CreateIndexFile = true;
formatter.Format(alignmentMap, outputfilePath);
Assert.IsTrue(File.Exists("BAMTests123.bam.bai"));
alignmentMap = parser.ParseOne <SequenceAlignmentMap>(outputfilePath);
Assert.IsNotNull(alignmentMap);
Assert.IsNotNull(alignmentMap.Header);
Assert.AreEqual(alignmentMap.Header.GetReferenceSequencesInfoFromSQHeader().Count, 1);
Assert.AreEqual(alignmentMap.Header.ReferenceSequences.Count, 1);
Assert.AreEqual(alignmentMap.QuerySequences.Count, 2);
alignmentMap = parser.ParseRange("BAMTests123.bam", new SequenceRange("chr20", 0, int.MaxValue));
Assert.IsNotNull(alignmentMap);
Assert.IsNotNull(alignmentMap.Header);
Assert.AreEqual(alignmentMap.Header.GetReferenceSequencesInfoFromSQHeader().Count, 1);
Assert.AreEqual(alignmentMap.Header.ReferenceSequences.Count, 1);
Assert.AreEqual(alignmentMap.QuerySequences.Count, 2);
alignmentMap = parser.ParseRange("BAMTests123.bam", new SequenceRange("chr20", 0, 28833));
Assert.IsNotNull(alignmentMap);
Assert.IsNotNull(alignmentMap.Header);
Assert.AreEqual(alignmentMap.Header.GetReferenceSequencesInfoFromSQHeader().Count, 1);
Assert.AreEqual(alignmentMap.Header.ReferenceSequences.Count, 1);
Assert.AreEqual(alignmentMap.QuerySequences.Count, 1);
File.Delete(outputfilePath);
File.Delete(outputIndexFile);
}
public void TestFormatter()
{
string filePath = @"TestData\BAM\SeqAlignment.bam";
string outputfilePath = "bamtest1.bam";
BAMParser parser = new BAMParser();
BAMFormatter formatter = new BAMFormatter();
SequenceAlignmentMap alignmentMap = parser.Parse(filePath);
Assert.IsTrue(alignmentMap != null);
Assert.AreEqual(alignmentMap.Header.GetReferenceSequences().Count, 1);
Assert.AreEqual(alignmentMap.QuerySequences.Count, 2);
formatter.Format(alignmentMap, outputfilePath);
formatter.CreateSortedBAMFile = true;
formatter.CreateIndexFile = true;
alignmentMap = parser.Parse(filePath);
formatter.Format(alignmentMap, "bamtest.bam");
Assert.IsTrue(File.Exists("bamtest.bam.bai"));
alignmentMap = parser.Parse(outputfilePath);
Assert.IsTrue(alignmentMap != null);
Assert.AreEqual(alignmentMap.Header.GetReferenceSequences().Count, 1);
Assert.AreEqual(alignmentMap.QuerySequences.Count, 2);
alignmentMap = parser.ParseRange("bamtest.bam", new SequenceRange("chr20", 0, int.MaxValue));
Assert.IsTrue(alignmentMap != null);
Assert.AreEqual(alignmentMap.Header.GetReferenceSequences().Count, 1);
Assert.AreEqual(alignmentMap.QuerySequences.Count, 2);
alignmentMap = parser.ParseRange("bamtest.bam", new SequenceRange("chr20", 0, 28833));
Assert.IsTrue(alignmentMap != null);
Assert.AreEqual(alignmentMap.Header.GetReferenceSequences().Count, 1);
Assert.AreEqual(alignmentMap.QuerySequences.Count, 1);
}
public static IEnumerable <ISequenceAlignmentParser> OutputAlignedMitoReadsFromBamFile(string Filename)
{
//Very inefficient right now
BAMParser bp = new BAMParser();
foreach (MitoBlastMatchRegion region in regionsThatMatch)
{
var map = bp.ParseRange(Filename, region.Contig, region.Start, region.End);
foreach (ISequence seq in map.QuerySequences.SelectMany(x => x.Sequences))
{
yield return(seq as ISequenceAlignmentParser);
}
}
}
/// <summary>
/// Parse BAM and validate parsed aligned sequences and its properties.
/// </summary>
/// <param name="nodeName">Different xml nodes used for different test cases</param>
/// <param name="BAMParserPam">BAM Parse method parameters</param>
/// <param name="IsEncoding">True for BAMParser ctor with encoding.
/// False otherwise </param>
void ValidateBAMParser(string nodeName,
BAMParserParameters BAMParserPam,
bool IsReferenceIndex)
{
// Get input and output values from xml node.
string bamFilePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string expectedAlignedSeqFilePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string refIndexValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.RefIndexNode);
string startIndexValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StartIndexNode);
string endIndexValue = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndIndexNode);
string alignedSeqCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlignedSeqCountNode);
string refSeqName = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ChromosomeNameNode);
SequenceAlignmentMap seqAlignment = null;
BAMParser bamParser = null;
try
{
bamParser = new BAMParser();
// Parse a BAM file with different parameters.
switch (BAMParserPam)
{
case BAMParserParameters.StreamReader:
using (Stream stream = new FileStream(bamFilePath, FileMode.Open,
FileAccess.Read))
{
seqAlignment = bamParser.Parse(stream);
}
break;
case BAMParserParameters.FileName:
seqAlignment = bamParser.Parse(bamFilePath);
break;
case BAMParserParameters.ParseRangeFileName:
seqAlignment = bamParser.ParseRange(bamFilePath,
Convert.ToInt32(refIndexValue, (IFormatProvider)null));
break;
case BAMParserParameters.ParseRangeWithIndex:
seqAlignment = bamParser.ParseRange(bamFilePath,
Convert.ToInt32(refIndexValue, (IFormatProvider)null),
Convert.ToInt32(startIndexValue, (IFormatProvider)null),
Convert.ToInt32(endIndexValue, (IFormatProvider)null));
break;
case BAMParserParameters.ParseRangeUsingRefSeq:
seqAlignment = bamParser.ParseRange(bamFilePath, refSeqName);
break;
case BAMParserParameters.ParseRangeUsingRefSeqAndFlag:
seqAlignment = bamParser.ParseRange(bamFilePath, refSeqName);
break;
case BAMParserParameters.ParseRangeUsingRefSeqUsingIndex:
seqAlignment = bamParser.ParseRange(bamFilePath, refSeqName,
Convert.ToInt32(startIndexValue, (IFormatProvider)null),
Convert.ToInt32(endIndexValue, (IFormatProvider)null));
break;
case BAMParserParameters.ParseRangeUsingIndexesAndFlag:
seqAlignment = bamParser.ParseRange(bamFilePath, refSeqName,
Convert.ToInt32(startIndexValue, (IFormatProvider)null),
Convert.ToInt32(endIndexValue, (IFormatProvider)null));
break;
}
// Validate BAM Header record fileds.
if (!IsReferenceIndex)
{
ValidateBAMHeaderRecords(nodeName, seqAlignment);
}
IList <SAMAlignedSequence> alignedSeqs = seqAlignment.QuerySequences;
Assert.AreEqual(alignedSeqCount, alignedSeqs.Count.ToString((IFormatProvider)null));
// Get expected sequences
using (FastAParser parserObj = new FastAParser(expectedAlignedSeqFilePath))
{
IEnumerable <ISequence> expectedSequences = parserObj.Parse();
IList <ISequence> expectedSequencesList = expectedSequences.ToList();
// Validate aligned sequences from BAM file.
for (int index = 0; index < alignedSeqs.Count; index++)
{
Assert.AreEqual(
new string(expectedSequencesList[index].Select(a => (char)a).ToArray()),
new string(alignedSeqs[index].QuerySequence.Select(a => (char)a).ToArray()));
// Log to NUNIT GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"BAM Parser BVT : Validated Aligned sequence :{0} successfully",
alignedSeqs[index].QuerySequence.ToString()));
Console.WriteLine(string.Format((IFormatProvider)null,
"BAM Parser BVT : Validated the aligned sequence :{0} successfully",
alignedSeqs[index].QuerySequence.ToString()));
}
}
}
finally
{
bamParser.Dispose();
}
}
