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()
{
const string filePath = @"TestUtils\BAM\SeqAlignment.bam";
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 ValidateBAMRangeQuery()
{
// Get input and output values from xml node.
string BAMStoragePath = this.utilityObj.xmlUtil.GetTextValue(
Constants.BAMHumanLargeNode, Constants.FilePathNode);
var bp=new BAMParser();
var m = bp.ParseRange(BAMStoragePath, "MT");
var names = m.QuerySequences.Select(x => x.RName).Distinct().ToList();
var all = m.QuerySequences.Select(x => x).Distinct().ToList();
var tot = m.QuerySequences.Select(x => x.QName).Distinct().ToList();
var toTest = new[] {new RangeQuery("MT",1,100,48),
new RangeQuery("1",0,Int32.MaxValue,45),
new RangeQuery("11",0,Int32.MaxValue,2),
new RangeQuery("MT",0,Int32.MaxValue,4335),
new RangeQuery("MT",16300,16500,92) };//Last one is on a 2^14 boundary
foreach (var r in toTest)
{
var res = bp.ParseRange(BAMStoragePath, r.RName, r.start, r.End);
Assert.AreEqual(r.ExpectedReturns, res.QuerySequences.Count);
}
}
/// <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>
private void ValidateBAMParser(string nodeName,
BAMParserParameters BAMParserPam,
bool IsReferenceIndex)
{
// Get input and output values from xml node.
string bamFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string expectedAlignedSeqFilePath = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string refIndexValue = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.RefIndexNode);
string startIndexValue = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.StartIndexNode);
string endIndexValue = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EndIndexNode);
string alignedSeqCount = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlignedSeqCountNode);
string refSeqName = this.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.ParseOne(stream);
}
break;
case BAMParserParameters.FileName:
seqAlignment = bamParser.ParseOne<SequenceAlignmentMap>(bamFilePath);
break;
case BAMParserParameters.ParseRangeFileName:
seqAlignment = bamParser.ParseRange(bamFilePath,
Convert.ToInt32(refIndexValue, null));
break;
case BAMParserParameters.ParseRangeWithIndex:
seqAlignment = bamParser.ParseRange(bamFilePath,
Convert.ToInt32(refIndexValue, null),
Convert.ToInt32(startIndexValue, null),
Convert.ToInt32(endIndexValue, 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, null),
Convert.ToInt32(endIndexValue, null));
break;
case BAMParserParameters.ParseRangeUsingIndexesAndFlag:
seqAlignment = bamParser.ParseRange(bamFilePath, refSeqName,
Convert.ToInt32(startIndexValue, null),
Convert.ToInt32(endIndexValue, null));
break;
}
// Validate BAM Header record fileds.
if (!IsReferenceIndex)
{
this.ValidateBAMHeaderRecords(nodeName, seqAlignment);
}
IList<SAMAlignedSequence> alignedSeqs = seqAlignment.QuerySequences;
Assert.AreEqual(alignedSeqCount, alignedSeqs.Count.ToString((IFormatProvider) null));
// Get expected sequences
var parserObj = new FastAParser();
{
IEnumerable<ISequence> expectedSequences = parserObj.Parse(expectedAlignedSeqFilePath);
IList<ISequence> expectedSequencesList = expectedSequences.ToList();
// Validate aligned sequences from BAM file.
for (int index = 0; index < alignedSeqs.Count; index++)
{
Assert.IsFalse(alignedSeqs[index].IsDummyRead);
Assert.AreEqual(
new string(expectedSequencesList[index].Select(a => (char) a).ToArray()),
new string(alignedSeqs[index].QuerySequence.Select(a => (char) a).ToArray()));
// Log to VSTest GUI.
ApplicationLog.WriteLine(string.Format(null,
"BAM Parser BVT : Validated Aligned sequence :{0} successfully",
alignedSeqs[index].QuerySequence));
}
}
}
finally
{
bamParser.Dispose();
}
}
/// <summary>
/// Parse BAM and validate parsed aligned sequences by creating
/// ISequenceAlignment interface object and its properties.
/// </summary>
/// <param name="nodeName">Different xml nodes used for different test cases</param>
/// <param name="BAMParserPam">BAM Parse method parameters</param>
private void InValidateSeqAlignmentMapBAMParser(string nodeName,
BAMParserParameters BAMParserPam)
{
// Get input and output values from xml node.
string bamFilePath = _utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string exception = string.Empty;
using (var bamParser = new BAMParser())
{
// Parse a BAM file with different parameters.
switch (BAMParserPam)
{
case BAMParserParameters.StreamReader:
try
{
bamParser.Parse(null as Stream);
Assert.Fail();
}
catch (ArgumentNullException ex)
{
exception = ex.Message;
}
try
{
using (Stream stream = new FileStream(bamFilePath, FileMode.Open, FileAccess.Read))
{
bamParser.Parse(stream).ToList();
Assert.Fail();
}
}
catch (Exception ex)
{
exception = ex.Message;
}
break;
case BAMParserParameters.FileName:
try
{
bamParser.Parse(null as string).First();
Assert.Fail();
}
catch (ArgumentNullException ex)
{
exception = ex.Message;
}
break;
case BAMParserParameters.ParseRangeWithIndex:
try
{
bamParser.ParseRange(null, 0);
Assert.Fail();
}
catch (ArgumentNullException ex)
{
exception = ex.Message;
}
try
{
bamParser.ParseRange(bamFilePath, -2);
Assert.Fail();
}
catch (ArgumentOutOfRangeException ex)
{
exception = ex.Message;
}
break;
case BAMParserParameters.ParseRangeFileName:
try
{
bamParser.ParseRange(null, new SequenceRange("chr20", 0, 10));
Assert.Fail();
}
catch (ArgumentNullException ex)
{
exception = ex.Message;
}
try
{
bamParser.ParseRange(bamFilePath, null as SequenceRange);
Assert.Fail();
}
catch (ArgumentNullException ex)
{
exception = ex.Message;
}
break;
default:
break;
}
// Log to VSTest GUI.
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully", exception));
}
}
