/// <summary>
/// Parses specified BAM file using index file.
/// Index file is assumed to be in the same location as that of the specified bam file with the name "filename".bai
/// For example, if the specified bam file name is D:\BAMdata\sample.bam then index file name will be taken as D:\BAMdata\sample.bam.bai
/// If index file is not available then this method throw an exception.
/// </summary>
/// <param name="parser">BAM parser</param>
/// <param name="fileName">BAM file name.</param>
/// <param name="refSeqName">Name of reference sequence.</param>
/// <returns>SequenceAlignmentMap object which contains alignments for specified reference sequence.</returns>
public static SequenceAlignmentMap ParseRange(this BAMParser parser, string fileName, string refSeqName)
{
if (parser == null)
{
throw new ArgumentNullException("parser");
}
if (string.IsNullOrWhiteSpace(fileName))
{
throw new ArgumentNullException("fileName");
}
if (refSeqName == null)
{
throw new ArgumentNullException("refSeqName");
}
using (var bamStream = File.OpenRead(fileName))
{
string bamIndexFileName = GetBAMIndexFileName(fileName);
using (FileStream bamIndexFile = File.OpenRead(bamIndexFileName))
using (var bamIndexStorage = new BAMIndexStorage(bamIndexFile))
{
return parser.GetAlignment(bamStream, bamIndexStorage, refSeqName);
}
}
}
/// <summary>
/// Parses specified BAM file using index file.
/// Index file is assumed to be in the same location as that of the specified bam file with the name "filename".bai
/// For example, if the specified bam file name is D:\BAMdata\sample.bam then index file name will be taken as D:\BAMdata\sample.bam.bai
/// If index file is not available then this method throw an exception.
/// </summary>
/// <param name="parser">BAM parser</param>
/// <param name="fileName">BAM file name.</param>
/// <param name="refSeqName">Name of reference sequence.</param>
/// <returns>SequenceAlignmentMap object which contains alignments for specified reference sequence.</returns>
public static SequenceAlignmentMap ParseRange(this BAMParser parser, string fileName, string refSeqName)
{
if (parser == null)
{
throw new ArgumentNullException("parser");
}
if (string.IsNullOrWhiteSpace(fileName))
{
throw new ArgumentNullException("fileName");
}
if (refSeqName == null)
{
throw new ArgumentNullException("refSeqName");
}
using (var bamStream = File.OpenRead(fileName))
{
string bamIndexFileName = GetBAMIndexFileName(fileName);
using (FileStream bamIndexFile = File.OpenRead(bamIndexFileName))
using (var bamIndexStorage = new BAMIndexStorage(bamIndexFile))
{
return(parser.GetAlignment(bamStream, bamIndexStorage, refSeqName));
}
}
}
/// <summary>
/// Creates BAMIndex object from the specified BAM file and writes to specified BAMIndex file.
/// </summary>
/// <param name="compressedBAMStream"></param>
/// <param name="indexStorage"></param>
private static void CreateBAMIndexFile(Stream compressedBAMStream, BAMIndexStorage indexStorage)
{
var parser = new BAMParser();
BAMIndex bamIndex = parser.GetIndexFromBAMStorage(compressedBAMStream);
indexStorage.Write(bamIndex);
}
/// <summary>
/// Write out the given SequenceAlignmentMap to the file
/// </summary>
/// <param name="formatter">BAMFormatter</param>
/// <param name="sam">SequenceAlignmentMap</param>
/// <param name="filename">File to write to</param>
/// <param name="indexFilename">BAM index file</param>
public static void Format(this BAMFormatter formatter, ISequenceAlignment sam, string filename, string indexFilename)
{
if (formatter == null)
{
throw new ArgumentNullException("formatter");
}
if (sam == null)
{
throw new ArgumentNullException("sam");
}
if (string.IsNullOrWhiteSpace(filename))
{
throw new ArgumentNullException("filename");
}
if (string.IsNullOrWhiteSpace(indexFilename))
{
throw new ArgumentNullException("indexFilename");
}
if (filename == indexFilename)
{
throw new ArgumentException("Use different filenames for index and alignment.", "indexFilename");
}
using (var fs = File.Create(filename))
using (var bamIndexFile = new BAMIndexStorage(File.Create(indexFilename)))
{
formatter.Format(fs, bamIndexFile, sam);
}
}
/// <summary>
/// Write out the given SequenceAlignmentMap to the file
/// </summary>
/// <param name="formatter">BAMFormatter</param>
/// <param name="sam">SequenceAlignmentMap</param>
/// <param name="filename">File to write to</param>
public static void Format(this BAMFormatter formatter, SequenceAlignmentMap sam, string filename)
{
if (formatter == null)
{
throw new ArgumentNullException("formatter");
}
if (sam == null)
{
throw new ArgumentNullException("sam");
}
if (string.IsNullOrWhiteSpace(filename))
{
throw new ArgumentNullException("filename");
}
using (var fs = File.Create(filename))
{
// Create the IndexFile if necessary
if (formatter.CreateIndexFile)
{
using (var bamIndexFile = new BAMIndexStorage(
File.Create(filename + Properties.Resource.BAM_INDEXFILEEXTENSION)))
{
formatter.Format(fs, bamIndexFile, sam);
}
}
else
{
formatter.Format(fs, sam);
}
}
}
/// <summary>
/// Write out the given SequenceAlignmentMap to the file
/// </summary>
/// <param name="formatter">BAMFormatter</param>
/// <param name="sam">SequenceAlignmentMap</param>
/// <param name="filename">File to write to</param>
public static void Format(this BAMFormatter formatter, SequenceAlignmentMap sam, string filename)
{
if (formatter == null)
{
throw new ArgumentNullException("formatter");
}
if (sam == null)
{
throw new ArgumentNullException("sam");
}
if (string.IsNullOrWhiteSpace(filename))
{
throw new ArgumentNullException("filename");
}
using (var fs = File.Create(filename))
{
// Create the IndexFile if necessary
if (formatter.CreateIndexFile)
{
using (var bamIndexFile = new BAMIndexStorage(
File.Create(filename + Properties.Resource.BAM_INDEXFILEEXTENSION)))
{
formatter.Format(fs, bamIndexFile, sam);
}
}
else
{
formatter.Format(fs, sam);
}
}
}
/// <summary>
/// Write out the given SequenceAlignmentMap to the file
/// </summary>
/// <param name="formatter">BAMFormatter</param>
/// <param name="sam">SequenceAlignmentMap</param>
/// <param name="filename">File to write to</param>
/// <param name="indexFilename">BAM index file</param>
public static void Format(this BAMFormatter formatter, ISequenceAlignment sam, string filename, string indexFilename)
{
if (formatter == null)
{
throw new ArgumentNullException("formatter");
}
if (sam == null)
{
throw new ArgumentNullException("sam");
}
if (string.IsNullOrWhiteSpace(filename))
{
throw new ArgumentNullException("filename");
}
if (string.IsNullOrWhiteSpace(indexFilename))
{
throw new ArgumentNullException("indexFilename");
}
if (filename == indexFilename)
{
throw new ArgumentException("Use different filenames for index and alignment.", "indexFilename");
}
using (var fs = File.Create(filename))
using (var bamIndexFile = new BAMIndexStorage(File.Create(indexFilename)))
{
formatter.Format(fs, bamIndexFile, sam);
}
}
static void CreateBAMIndexFile(string bamFileName, string indexFileName)
{
using (var bamStream = File.OpenRead(bamFileName))
using (var indexStream = File.Create(indexFileName))
using (var indexStorage = new BAMIndexStorage(indexStream))
{
BAMIndex indexFromBamStorage = new BAMParser().GetIndexFromBAMStorage(bamStream);
indexStorage.Write(indexFromBamStorage);
}
}
internal LinearIndexArrayMaker(int refSeqLength)
{
int size;
if (refSeqLength <= 0)
{
size = BAMIndexStorage.MaxLinerindexArraySize;
}
else
{
size = BAMIndexStorage.LargestBinPossibleForSequenceLength(refSeqLength);
}
//TODO: Plus one now because weird things could happen with alignment length such that the bin is one higher
//never seen this, but not sure it can't happen.
offSetArray = new FileOffset[size + 1];
}
/// <summary>
/// Writes specified alignment object to a stream.
/// The output is formatted according to the BAM specification.
/// </summary>
/// <param name="writer">Stream to write BAM data.</param>
/// <param name="indexWriter">BAMIndexFile to write index data.</param>
/// <param name="sequenceAlignment">SequenceAlignmentMap object.</param>
public void Format(Stream writer, BAMIndexStorage indexWriter, ISequenceAlignment sequenceAlignment)
{
if (sequenceAlignment == null)
{
throw new ArgumentNullException("sequenceAlignment");
}
if (writer == null)
{
throw new ArgumentNullException("writer");
}
if (indexWriter == null)
{
throw new ArgumentNullException("indexWriter");
}
WriteSequenceAlignment(sequenceAlignment, writer, indexWriter);
}
/// <summary>
/// Parses specified BAM file using index file.
/// </summary>
/// <param name="parser">BAM parser</param>
/// <param name="fileName">BAM file name.</param>
/// <param name="range">SequenceRange object which contains reference sequence name and start and end co-ordinates.</param>
/// <returns>SequenceAlignmentMap object which contains alignments for specified reference sequence and for specified range.</returns>
public static SequenceAlignmentMap ParseRange(this BAMParser parser, string fileName, SequenceRange range)
{
if (parser == null)
{
throw new ArgumentNullException("parser");
}
if (string.IsNullOrWhiteSpace(fileName))
{
throw new ArgumentNullException("fileName");
}
if (range == null)
{
throw new ArgumentNullException("range");
}
if (string.IsNullOrEmpty(range.ID))
{
throw new ArgumentException("Reference sequence name (range.ID) can't empty or null.");
}
int start = range.Start >= int.MaxValue ? int.MaxValue : (int)range.Start;
int end = range.End >= int.MaxValue ? int.MaxValue : (int)range.End;
using (FileStream bamStream = File.OpenRead(fileName))
{
string bamIndexFileName = GetBAMIndexFileName(fileName);
using (FileStream bamIndexFile = File.OpenRead(bamIndexFileName))
using (BAMIndexStorage bamIndexStorage = new BAMIndexStorage(bamIndexFile))
{
if (start == 0 && end == int.MaxValue)
{
return(parser.GetAlignment(bamStream, bamIndexStorage, range.ID));
}
return(parser.GetAlignment(bamStream, bamIndexStorage, range.ID, start, end));
}
}
}
/// <summary>
/// Writes specified alignment object to a stream.
/// The output is formatted according to the BAM specification.
/// </summary>
/// <param name="writer">Stream to write BAM data.</param>
/// <param name="indexWriter">BAMIndexFile to write index data.</param>
/// <param name="sequenceAlignment">SequenceAlignmentMap object.</param>
public void Format(Stream writer, BAMIndexStorage indexWriter, ISequenceAlignment sequenceAlignment)
{
if (sequenceAlignment == null)
{
throw new ArgumentNullException("sequenceAlignment");
}
if (writer == null)
{
throw new ArgumentNullException("writer");
}
if (indexWriter == null)
{
throw new ArgumentNullException("indexWriter");
}
WriteSequenceAlignment(sequenceAlignment, writer, indexWriter);
}
/// <summary>
/// Format BAM file and validate.
/// </summary>
/// <param name="nodeName">Different xml nodes used for different test cases</param>
/// <param name="BAMParserPam">BAM Format method parameters</param>
void ValidateBAMFormatter(string nodeName,
BAMParserParameters BAMParserPam)
{
// Get input and output values from xml node.
string BAMStoragePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string expectedAlignedSeqFilePath = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alignedSeqCount = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlignedSeqCountNode);
SequenceAlignmentMap seqAlignment = null;
try {
using (BAMIndexStorage BAMIndexStorageObj = new BAMIndexStorage(
File.Create(Constants.BAMTempIndexFileForIndexData)))
{
// Parse a BAM file.
BAMParser bamParserObj = new BAMParser();
seqAlignment = bamParserObj.ParseOne<SequenceAlignmentMap>(BAMStoragePath);
// Create a BAM formatter object.
BAMFormatter formatterObj = new BAMFormatter();
// Write/Format aligned sequences to BAM file.
switch (BAMParserPam)
{
case BAMParserParameters.StreamAndIndexFile:
using (Stream stream = new FileStream(Constants.BAMTempFileName,
FileMode.Create, FileAccess.ReadWrite))
{
formatterObj.Format(stream, BAMIndexStorageObj, seqAlignment);
}
break;
default:
break;
}
// Parse formatted BAM file and validate aligned sequences.
SequenceAlignmentMap expectedSeqAlignmentMap = bamParserObj.ParseOne<SequenceAlignmentMap>(
Constants.BAMTempFileName);
// Validate Parsed BAM file Header record fields.
this.ValidateBAMHeaderRecords(nodeName, expectedSeqAlignmentMap);
IList<SAMAlignedSequence> alignedSeqs = expectedSeqAlignmentMap.QuerySequences;
Assert.AreEqual(alignedSeqCount, alignedSeqs.Count.ToString((IFormatProvider)null));
// Get expected sequences
FastAParser 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.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((IFormatProvider)null,
"BAM Formatter P1 : Validated Aligned sequence :{0} successfully",
alignedSeqs[index].QuerySequence.ToString()));
}
}
}
finally
{
File.Delete(Constants.BAMTempFileName);
File.Delete(Constants.BAMTempIndexFile);
}
}
public void ValidateBAMIndexMatchesExpectation()
{
// Get input and output values from xml node.
string BAMStoragePath = this.utilityObj.xmlUtil.GetTextValue(
Constants.BAMHumanLargeNode, Constants.FilePathNode);
string expectedIndexPath= this.utilityObj.xmlUtil.GetTextValue(
Constants.BAMHumanLargeNode, Constants.BAMIndexFileNode);
var bp = new BAMParser();
//get observed index file
BAMIndex bi;
using (Stream bamStream = new FileStream(BAMStoragePath, FileMode.Open, FileAccess.Read))
{
bi = bp.GetIndexFromBAMStorage(bamStream);
}
//get expected
var bi2 = new BAMIndexStorage(File.OpenRead(expectedIndexPath)).Read();
//now verify
Assert.AreEqual(bi2.RefIndexes.Count, bi.RefIndexes.Count);
for (int i = 0; i < bi.RefIndexes.Count; i++)
{
var obs = bi.RefIndexes[i];
var exp = bi2.RefIndexes[i];
Assert.AreEqual(obs.Bins.Count, exp.Bins.Count);
Assert.AreEqual(obs.LinearIndex.Count, exp.LinearIndex.Count);
Assert.AreEqual(obs.MappedReadsCount, exp.MappedReadsCount);
Assert.AreEqual(obs.UnMappedReadsCount, exp.UnMappedReadsCount);
var ob = obs.Bins.ToList();
var eb = exp.Bins.ToList();
ob.Sort((x, y) => x.BinNumber.CompareTo(y.BinNumber));
eb.Sort((x, y) => x.BinNumber.CompareTo(y.BinNumber));
for (int j = 0; j < ob.Count; j++)
{
var obb=ob[0];
var ebb=eb[0];
Assert.AreEqual(obb.BinNumber, ebb.BinNumber);
Assert.AreEqual(obb.Chunks.Count, ebb.Chunks.Count);
var c1 = obb.Chunks.ToList();
var c2 = ebb.Chunks.ToList();
c1.Sort((x, y) => x.ChunkStart.CompareTo(y.ChunkStart));
c2.Sort((x, y) => x.ChunkStart.CompareTo(y.ChunkStart));
for (int k = 0; k < c1.Count; k++)
{
var co = c1[k];
var eo = c2[k];
Assert.AreEqual(eo.ChunkStart, co.ChunkStart);
Assert.AreEqual(eo.ChunkEnd, co.ChunkEnd);
}
}
}
}
/// <summary>
/// Writes sequence alignment to specified stream.
/// </summary>
/// <param name="sequenceAlignment">Sequence alignment object</param>
/// <param name="writer">Stream to write.</param>
/// <param name="indexStorage">BAMIndex file.</param>
private void WriteSequenceAlignment(ISequenceAlignment sequenceAlignment, Stream writer, BAMIndexStorage indexStorage)
{
// validate sequenceAlignment.
SequenceAlignmentMap sequenceAlignmentMap = ValidateAlignment(sequenceAlignment);
// write bam struct to temp file.
using (var fstemp = PlatformManager.Services.CreateTempStream())
{
WriteUncompressed(sequenceAlignmentMap, fstemp, CreateSortedBAMFile);
fstemp.Seek(0, SeekOrigin.Begin);
// Compress and write to the specified stream.
CompressBAMFile(fstemp, writer);
}
// if index file need to be created.
if (indexStorage != null)
{
writer.Seek(0, SeekOrigin.Begin);
CreateBAMIndexFile(writer, indexStorage);
}
}
/// <summary>
/// Format BAM file using IsequenceAlignment object.
/// </summary>
/// <param name="nodeName">Different xml nodes used for different test cases</param>
/// <param name="BAMParserPam">BAM Format method parameters</param>
/// <param name="WriteBAMIndexData">True if writting BAM index data to BAMIndex file,
/// false otherwise</param>
/// <param name="IsNotSupportedMethods">True if validating notsuportedMethods,
/// false otherwise</param>
void ValidateBAMFormatterWithSequenceAlignment(string nodeName,
BAMParserParameters BAMParserPam, bool WriteBAMIndexData,
bool IsNotSupportedMethods)
{
// Get input and output values from xml node.
string BAMStoragePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string expectedAlignedSeqFilePath = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string alignedSeqCount = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.AlignedSeqCountNode);
BAMIndexStorage BAMIndexStorageObj = null;
ISequenceAlignmentParser bamParserObj = new BAMParser();
try
{
using (BAMParser bamSeqMapParserObj = new BAMParser())
{
IEnumerable<ISequenceAlignment> seqList = bamParserObj.Parse(BAMStoragePath);
try
{
// Write BAm index data to BAM Index File.
if (WriteBAMIndexData)
{
BAMIndexStorageObj = new BAMIndexStorage(
File.Create(Constants.BAMTempIndexFileForSequenceAlignment));
}
// Create a BAM formatter object.
BAMFormatter formatterObj = new BAMFormatter
{
CreateSortedBAMFile = true,
CreateIndexFile = true
};
// Write/Format aligned sequences to BAM file.
switch (BAMParserPam)
{
case BAMParserParameters.StreamWriter:
try
{
using (var writer = File.Create(Constants.BAMTempFileName))
{
foreach (ISequenceAlignment seq in seqList)
{
formatterObj.Format(writer, seq);
Assert.Fail();
}
}
}
catch (NotSupportedException ex)
{
string message = ex.Message;
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"BAM Formatter P1 : Validated the exception {0} successfully"
, message));
}
break;
case BAMParserParameters.Stream:
using (Stream stream = new
FileStream(Constants.BAMTempFileName,
FileMode.OpenOrCreate, FileAccess.ReadWrite))
{
foreach (ISequenceAlignment seq in seqList)
{
formatterObj.Format(stream, seq);
}
}
File.Exists(Constants.BAMTempFileName);
break;
case BAMParserParameters.FileName:
foreach (ISequenceAlignment seq in seqList)
{
formatterObj.Format(seq, Constants.BAMTempFileName);
}
File.Exists(Constants.BAMTempFileName);
break;
case BAMParserParameters.StreamAndIndexFile:
using (Stream stream = new
FileStream(Constants.BAMTempFileName,
FileMode.Create, FileAccess.ReadWrite))
{
foreach (ISequenceAlignment seq in seqList)
{
formatterObj.Format(stream, BAMIndexStorageObj, seq);
}
}
File.Exists(Constants.BAMTempFileName);
break;
case BAMParserParameters.IndexFile:
foreach (ISequenceAlignment seq in seqList)
{
formatterObj.Format(seq, Constants.BAMTempFileName,
Constants.BAMTempIndexFile);
}
File.Exists(Constants.BAMTempFileName);
break;
default:
break;
}
if (!IsNotSupportedMethods)
{
// Parse formatted BAM file and validate aligned sequences.
SequenceAlignmentMap expectedSeqAlignmentMap = bamSeqMapParserObj.ParseOne<SequenceAlignmentMap>(
Constants.BAMTempFileName);
IList<SAMAlignedSequence> alignedSeqs = expectedSeqAlignmentMap.QuerySequences;
Assert.AreEqual(alignedSeqCount, alignedSeqs.Count.ToString((IFormatProvider)null));
// Get expected sequences
FastAParser 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.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((IFormatProvider)null,
"BAM Formatter P1 : Validated Aligned sequence :{0} successfully",
alignedSeqs[index].QuerySequence.ToString()));
}
}
}
finally
{
if (BAMIndexStorageObj != null)
BAMIndexStorageObj.Dispose();
}
}
}
finally
{
(bamParserObj as BAMParser).Dispose();
File.Delete(Constants.BAMTempFileName);
File.Delete(Constants.BAMTempIndexFile);
}
}
public void InvalidateBAMIndexStorage()
{
//set source stream as null
try
{
var biFile = new BAMIndexStorage(null);
Assert.Fail();
}
catch (ArgumentNullException ex)
{
ApplicationLog.Write("BAM P2 : Successfully caught ArgumentNullException : " + ex.Message);
}
try
{
string temp = null;
using (var biFile = new BAMIndexStorage(File.Create(temp)))
{
Assert.Fail();
}
}
catch (ArgumentNullException ex)
{
ApplicationLog.Write("BAM P2 : Successfully caught ArgumentNullException : " + ex.Message);
}
}
/// <summary>
/// Parses specified BAM file using index file.
/// </summary>
/// <param name="parser">BAM parser</param>
/// <param name="fileName">BAM file name.</param>
/// <param name="range">SequenceRange object which contains reference sequence name and start and end co-ordinates.</param>
/// <returns>SequenceAlignmentMap object which contains alignments for specified reference sequence and for specified range.</returns>
public static SequenceAlignmentMap ParseRange(this BAMParser parser, string fileName, SequenceRange range)
{
if (parser == null)
{
throw new ArgumentNullException("parser");
}
if (string.IsNullOrWhiteSpace(fileName))
{
throw new ArgumentNullException("fileName");
}
if (range == null)
{
throw new ArgumentNullException("range");
}
if (string.IsNullOrEmpty(range.ID))
{
throw new ArgumentException("Reference sequence name (range.ID) can't empty or null.");
}
int start = range.Start >= int.MaxValue ? int.MaxValue : (int)range.Start;
int end = range.End >= int.MaxValue ? int.MaxValue : (int)range.End;
using (FileStream bamStream = File.OpenRead(fileName))
{
string bamIndexFileName = GetBAMIndexFileName(fileName);
using (FileStream bamIndexFile = File.OpenRead(bamIndexFileName))
using (BAMIndexStorage bamIndexStorage = new BAMIndexStorage(bamIndexFile))
{
if (start == 0 && end == int.MaxValue)
return parser.GetAlignment(bamStream, bamIndexStorage, range.ID);
return parser.GetAlignment(bamStream, bamIndexStorage, range.ID, start, end);
}
}
}
/// <summary>
/// Format BAM file and validate.
/// </summary>
/// <param name="nodeName">Different xml nodes used for different test cases</param>
private void InValidateBAMFormatter(string nodeName)
{
// Get input and output values from xml node.
string bamFilePath = _utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
using (var bamParserObj = new BAMParser())
{
using (var storage = new BAMIndexStorage(File.Create(Constants.BAMTempIndexFileForIndexData)))
{
// Parse a BAM file.
var seqAlignment = bamParserObj.ParseOne <SequenceAlignmentMap>(bamFilePath);
// Create a BAM formatter object.
var formatterObj = new BAMFormatter();
// Null filename
try
{
formatterObj.Format(seqAlignment, null, Constants.BAMTempIndexFileForIndexData);
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully", ex.Message));
}
// Same filename
try
{
formatterObj.Format(seqAlignment, Constants.BAMTempFileName, Constants.BAMTempFileName);
}
catch (ArgumentException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully", ex.Message));
}
// Null sequence
try
{
formatterObj.Format(null, bamFilePath, Constants.BAMTempIndexFileForIndexData);
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully", ex.Message));
}
// Null index
try
{
formatterObj.Format(seqAlignment, bamFilePath, null);
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully", ex.Message));
}
// Invalidate BAM Parser Format(SeqAlignmentMap, BamFileName)
try
{
formatterObj.Format(null as SequenceAlignmentMap,
Constants.BAMTempFileName);
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully", ex.Message));
}
try
{
formatterObj.Format(seqAlignment, null as string);
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully", ex.Message));
}
// Invalidate Format(SequenceAlignmentMap, StreamWriter)
try
{
formatterObj.Format(null, seqAlignment);
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully", ex.Message));
}
Stream stream;
try
{
using (stream = new FileStream(Constants.BAMTempFileName, FileMode.OpenOrCreate, FileAccess.ReadWrite))
{
formatterObj.Format(stream, null as ISequenceAlignment);
}
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully", ex.Message));
}
// Invalidate Format(SequenceAlignmentMap, StreamWriter, IndexFile)
try
{
formatterObj.Format(null, storage, seqAlignment);
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully", ex.Message));
}
try
{
using (stream = new FileStream(Constants.BAMTempFileName, FileMode.OpenOrCreate, FileAccess.ReadWrite))
{
formatterObj.Format(stream, storage, null);
}
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully", ex.Message));
}
try
{
using (stream = new FileStream(Constants.BAMTempFileName, FileMode.OpenOrCreate, FileAccess.ReadWrite))
{
formatterObj.Format(stream, null, seqAlignment);
}
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully", ex.Message));
}
formatterObj = null;
}
}
}
/// <summary>
/// Format BAM file using IsequenceAlignment object.
/// </summary>
/// <param name="nodeName">Different xml nodes used for different test cases</param>
private void InValidateBAMFormatterWithSequenceAlignment(string nodeName)
{
// Get input and output values from xml node.
string bamFilePath = _utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
ISequenceAlignmentParser bamParserObj = new BAMParser();
IList<ISequenceAlignment> seqList = bamParserObj.Parse(bamFilePath).ToList();
try
{
using (var BAMIndexStorageObj = new BAMIndexStorage(File.Create(Constants.BAMTempIndexFileForInvalidData)))
{
// Create a BAM formatter object.
var formatterObj = new BAMFormatter();
InvalidateBAmFormatter(formatterObj, seqList);
InvalidateBAmFormatterWithWithInvalidValues(formatterObj,seqList, bamFilePath, BAMIndexStorageObj);
InvalidateBAmFormatterWithWithNullValues(formatterObj,seqList);
}
}
finally
{
(bamParserObj as BAMParser).Dispose();
File.Delete(Constants.BAMTempIndexFileForInvalidData);
}
}
/// <summary>
/// Writes sequence alignment to specified stream.
/// </summary>
/// <param name="sequenceAlignment">Sequence alignment object</param>
/// <param name="writer">Stream to write.</param>
/// <param name="indexStorage">BAMIndex file.</param>
private void WriteSequenceAlignment(ISequenceAlignment sequenceAlignment, Stream writer, BAMIndexStorage indexStorage)
{
// validate sequenceAlignment.
SequenceAlignmentMap sequenceAlignmentMap = ValidateAlignment(sequenceAlignment);
// write bam struct to temp file.
using (var fstemp = PlatformManager.Services.CreateTempStream())
{
WriteUncompressed(sequenceAlignmentMap, fstemp, CreateSortedBAMFile);
fstemp.Seek(0, SeekOrigin.Begin);
// Compress and write to the specified stream.
CompressBAMFile(fstemp, writer);
}
// if index file need to be created.
if (indexStorage != null)
{
writer.Seek(0, SeekOrigin.Begin);
CreateBAMIndexFile(writer, indexStorage);
}
}
/// <summary>
/// Creates BAMIndex object from the specified BAM file and writes to specified BAMIndex file.
/// </summary>
/// <param name="compressedBAMStream"></param>
/// <param name="indexStorage"></param>
private static void CreateBAMIndexFile(Stream compressedBAMStream, BAMIndexStorage indexStorage)
{
var parser = new BAMParser();
BAMIndex bamIndex = parser.GetIndexFromBAMStorage(compressedBAMStream);
indexStorage.Write(bamIndex);
}
/// <summary>
/// Invalidate BAMFormatter with invalid values.
/// </summary>
/// <param name="formatterObj">Bam formatter obj</param>
/// <param name="seqList">List of sequences</param>
private static void InvalidateBAmFormatterWithWithInvalidValues(BAMFormatter formatterObj,
IList<ISequenceAlignment> seqList,
string bamFilePath, BAMIndexStorage BAMIndexStorageObj)
{
try
{
formatterObj.Format(null as ISequenceAlignment, bamFilePath,
Constants.BAMTempIndexFileForIndexData);
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully",
ex.Message));
}
try
{
foreach (ISequenceAlignment seq in seqList)
{
formatterObj.Format(seq, bamFilePath, null);
}
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully",
ex.Message));
}
// Invalidate Format(IseqAlignment, StreamWriter, IndexFile)
try
{
foreach (ISequenceAlignment seq in seqList)
{
formatterObj.Format(null, BAMIndexStorageObj, seq);
}
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully",
ex.Message));
}
try
{
using (Stream stream = new
FileStream(Constants.BAMTempFileName,
FileMode.OpenOrCreate, FileAccess.ReadWrite))
{
formatterObj.Format(stream, BAMIndexStorageObj, null as ISequenceAlignment);
}
}
catch (ArgumentNullException ex)
{
ApplicationLog.WriteLine(string.Format("BAM Parser P2 : Validated Exception {0} successfully",
ex.Message));
}
}