public void TestJump()
{
var smallBam = Path.Combine(TestPaths.LocalTestDataDirectory, "bwaXC.bam");
using (var reader = new BamReader(smallBam))
{
BamAlignment al = new BamAlignment();
Assert.True(reader.Jump(reader.GetReferenceIndex("chr1"), 20200));
Assert.True(reader.GetNextAlignment(ref al, true));
Assert.True(al.Position > 18000);
Assert.True(reader.Jump(reader.GetReferenceIndex("chr1"), 200));
Assert.True(reader.GetNextAlignment(ref al, true));
Assert.True(al.Position < 250);
// now, forward-only jumping
Assert.True(reader.JumpForward(reader.GetReferenceIndex("chr1"), 20200));
Assert.True(reader.GetNextAlignment(ref al, true));
Assert.True(al.Position > 18000); // a good forward jump
var position = reader.Tell();
Assert.True(reader.JumpForward(reader.GetReferenceIndex("chr1"), 200));
Assert.Equal(position, reader.Tell()); // we stayed put
Assert.True(reader.GetNextAlignment(ref al, true));
Assert.True(al.Position > 18000);
}
}
//wrapper should now handle all throwing and catching..
protected override void ProgramExecution()
{
var optionsUsed = _appOptionParser.ParsingResult.OptionsUsed;
var doNotPassToSubprocess = new List <string>()
{
"outFolder", "numProcesses", "exePath", "intermediateDir", "multiprocess", "chromosomes"
};
var cmdLineList = MultiProcessHelpers.GetCommandLineWithoutIgnoredArguments(optionsUsed, doNotPassToSubprocess);
var refNameMapping = new Dictionary <string, int>();
using (var bamReader = new BamReader(_options.InputBam))
{
var chroms = bamReader.GetReferenceNames();
foreach (var referenceName in chroms)
{
if (_options.Chromosomes != null && !_options.Chromosomes.ToList().Contains(referenceName))
{
continue;
}
refNameMapping.Add(referenceName, bamReader.GetReferenceIndex(referenceName));
}
}
var taskManager = new CliTaskManager(_options.NumProcesses);
var geminiProcessor = new GeminiMultiProcessor(_options, new CliTaskCreator());
var samtoolsWrapper = new SamtoolsWrapper(_options.GeminiOptions.SamtoolsPath, _options.GeminiOptions.IsWeirdSamtools);
geminiProcessor.Execute(taskManager, refNameMapping, cmdLineList, samtoolsWrapper);
}
private List <GenomeMetadata.SequenceMetadata> GetReferences(string inBam)
{
List <GenomeMetadata.SequenceMetadata> bamReferences;
var refIdMapping = new Dictionary <int, string>();
using (var reader = new BamReader(inBam))
{
bamReferences = reader.GetReferences();
foreach (var referenceName in reader.GetReferenceNames())
{
refIdMapping.Add(reader.GetReferenceIndex(referenceName), referenceName);
}
}
return(bamReferences);
}
private IReadPairHandler CreatePairHandler(ReadStatusCounter readStatuses)
{
var stitcher = new BasicStitcher(_options.MinBaseCallQuality, useSoftclippedBases: _options.UseSoftClippedBases,
nifyDisagreements: _options.NifyDisagreements, debug: _options.Debug, nifyUnstitchablePairs: _options.NifyUnstitchablePairs, ignoreProbeSoftclips: !_options.StitchProbeSoftclips, maxReadLength: _options.MaxReadLength);
var refIdMapping = new Dictionary <int, string>();
using (var reader = new BamReader(_inBam))
{
foreach (var referenceName in reader.GetReferenceNames())
{
refIdMapping.Add(reader.GetReferenceIndex(referenceName), referenceName);
}
}
return(new PairHandler(refIdMapping, stitcher, _options.FilterUnstitchablePairs, readStatuses));
}
private IBamWriter CreateBamWriter()
{
string bamHeader;
List <GenomeMetadata.SequenceMetadata> bamReferences;
var refIdMapping = new Dictionary <int, string>();
using (var reader = new BamReader(_inBam))
{
bamReferences = reader.GetReferences();
var oldBamHeader = reader.GetHeader();
bamHeader = UpdateBamHeader(oldBamHeader);
foreach (var referenceName in reader.GetReferenceNames())
{
refIdMapping.Add(reader.GetReferenceIndex(referenceName), referenceName);
}
}
return(new BamWriterWrapper(new BamWriter(_outBam, bamHeader, bamReferences)));
}
private IBamWriterMultithreaded CreateBamWriter()
{
string bamHeader;
List <GenomeMetadata.SequenceMetadata> bamReferences;
var refIdMapping = new Dictionary <int, string>();
using (var reader = new BamReader(_inBam))
{
bamReferences = reader.GetReferences();
var oldBamHeader = reader.GetHeader();
bamHeader = UpdateBamHeader(oldBamHeader);
foreach (var referenceName in reader.GetReferenceNames())
{
refIdMapping.Add(reader.GetReferenceIndex(referenceName), referenceName);
}
}
if (_options.SortMemoryGB <= 0)
{
return(new BamWriterMultithreaded(_outBam, bamHeader, bamReferences, _options.NumThreads, 1));
}
return(new BamWriterInMem(_outBam, bamHeader, bamReferences, _options.SortMemoryGB, _options.NumThreads, 1));
}
private List <IReadPairHandler> CreatePairHandlers(ReadStatusCounter readStatuses, int numThreads)
{
var handlers = new List <IReadPairHandler>(numThreads);
var refIdMapping = new Dictionary <int, string>();
using (var reader = new BamReader(_inBam))
{
foreach (var referenceName in reader.GetReferenceNames())
{
refIdMapping.Add(reader.GetReferenceIndex(referenceName), referenceName);
}
}
for (int i = 0; i < numThreads; ++i)
{
var stitcher = new BasicStitcher(_options.MinBaseCallQuality, useSoftclippedBases: _options.UseSoftClippedBases,
nifyDisagreements: _options.NifyDisagreements, debug: _options.Debug, nifyUnstitchablePairs: _options.NifyUnstitchablePairs, ignoreProbeSoftclips: !_options.StitchProbeSoftclips, maxReadLength: _options.MaxReadLength, ignoreReadsAboveMaxLength: _options.IgnoreReadsAboveMaxLength, minMapQuality: _options.FilterMinMapQuality, dontStitchHomopolymerBridge: _options.DontStitchHomopolymerBridge);
handlers.Add(new PairHandler(refIdMapping, stitcher, readStatuses, _options.FilterUnstitchablePairs, true));
}
return(handlers);
}
/// <summary>
/// Step 2: Get the ref and variant allele frequencies for the variants of interest, in the tumor bam file.
/// </summary>
protected void ProcessBamFile(string bamPath)
{
Console.WriteLine("{0} Looping over bam records from {1}", DateTime.Now, bamPath);
int overallCount = 0;
int nextVariantIndex = 0;
using (BamReader reader = new BamReader(bamPath))
{
BamAlignment read = new BamAlignment();
int refID = reader.GetReferenceIndex(this.Chromosome);
if (refID < 0)
{
throw new ArgumentException(string.Format("Error: Chromosome name '{0}' does not match bam file at '{1}'", this.Chromosome, bamPath));
}
Console.WriteLine("Jump to refid {0} {1}", refID, this.Chromosome);
reader.Jump(refID, 0);
while (true)
{
bool result = reader.GetNextAlignment(ref read, false);
if (!result)
{
break;
}
if (!read.HasPosition() || read.RefID > refID)
{
break; // We're past our chromosome of interest.
}
if (read.RefID < refID)
{
continue; // We're not yet on our chromosome of interest.
}
overallCount++;
if (overallCount % 1000000 == 0)
{
Console.WriteLine("Record {0} at {1}...", overallCount, read.Position);
}
// Skip over unaligned or other non-count-worthy reads:
if (!read.IsPrimaryAlignment())
{
continue;
}
if (!read.IsMapped())
{
continue;
}
if (read.IsDuplicate())
{
continue;
}
if (read.MapQuality <= MinimumMapQ)
{
continue;
}
// Scan forward through the variants list, to keep up with our reads:
while (nextVariantIndex < this.Variants.Count && this.Variants[nextVariantIndex].ReferencePosition < read.Position)
{
nextVariantIndex++;
}
if (nextVariantIndex >= this.Variants.Count)
{
break;
}
// If the read doesn't look like it has a reasonable chance of touching the next variant, continue:
if (read.Position + 1000 < this.Variants[nextVariantIndex].ReferencePosition)
{
continue;
}
// This read potentially overlaps next variant (and further variants). Count bases!
ProcessReadBases(read, nextVariantIndex);
}
}
Console.WriteLine("Looped over {0} bam records in all", overallCount);
}
/// <summary>
/// Bins fragments.
/// </summary>
private void binFragments()
{
// Sanity check: The BAM index file must exist, in order for us to seek to our target chromosome!
if (!Bam.Index.Exists)
{
throw new Exception(string.Format("Fatal error: Bam index not found at {0}", Bam.Index.FullName));
}
long pairedAlignmentCount = 0; // keep track of paired alignments
usableFragmentCount = 0;
using (BamReader reader = new BamReader(Bam.BamFile.FullName))
{
int desiredRefIndex = -1;
desiredRefIndex = reader.GetReferenceIndex(Chromosome);
if (desiredRefIndex == -1)
{
throw new Illumina.Common.IlluminaException(
string.Format("Unable to retrieve the reference sequence index for {0} in {1}.", Chromosome, Bam.BamFile.FullName));
}
bool result = reader.Jump(desiredRefIndex, 0);
if (!result)
{
// Note: This is not necessarily an error, it just means that there *are* no reads for this chromosome in this
// .bam file. That is not uncommon e.g. for truseq amplicon.
return;
}
Dictionary <string, int> readNameToBinIndex = new Dictionary <string, int>();
HashSet <string> samePositionReadNames = new HashSet <string>();
int binIndexStart = 0;
int prevPosition = -1;
BamAlignment alignment = new BamAlignment();
while (reader.GetNextAlignment(ref alignment, true))
{
int refID = alignment.RefID;
// quit if the current reference index is different from the desired reference index
if (refID != desiredRefIndex)
{
break;
}
if (refID == -1)
{
continue;
}
if (alignment.Position < prevPosition) // Make sure the BAM is properly sorted
{
throw new Illumina.Common.IlluminaException(
string.Format("The alignment on {0} are not properly sorted in {1}: {2}", Chromosome, Bam.BamFile.FullName, alignment.Name));
}
prevPosition = alignment.Position;
if (alignment.IsPaired())
{
pairedAlignmentCount++;
}
BinOneAlignment(alignment, FragmentBinnerConstants.MappingQualityThreshold, readNameToBinIndex,
samePositionReadNames, ref usableFragmentCount, Bins, ref binIndexStart);
}
}
if (pairedAlignmentCount == 0)
{
throw new Illumina.Common.IlluminaException(string.Format("No paired alignments found for {0} in {1}", Chromosome, Bam.BamFile.FullName));
}
}
/// <summary>
/// Reads in a bam file and marks within the BitArrays which genomic mers are present.
/// </summary>
/// <param name="bamFile">bam file read alignments from.</param>
/// <param name="observedAlignments">Dictioanry of BitArrays, one for each chromosome, to store the alignments in.</param>
static void LoadObservedAlignmentsBAM(string bamFile, bool isPairedEnd, string chromosome, CanvasCoverageMode coverageMode, HitArray observed, Int16[] fragmentLengths)
{
// Sanity check: The .bai file must exist, in order for us to seek to our target chromosome!
string indexPath = bamFile + ".bai";
if (!File.Exists(indexPath))
{
throw new Exception(string.Format("Fatal error: Bam index not found at {0}", indexPath));
}
using (BamReader reader = new BamReader(bamFile))
{
int desiredRefIndex = -1;
desiredRefIndex = reader.GetReferenceIndex(chromosome);
if (desiredRefIndex == -1)
{
throw new ApplicationException(
string.Format("Unable to retrieve the reference sequence index for {0} in {1}.", chromosome,
bamFile));
}
bool result = reader.Jump(desiredRefIndex, 0);
if (!result)
{
// Note: This is not necessarily an error, it just means that there *are* no reads for this chromosome in this
// .bam file. That is not uncommon e.g. for truseq amplicon.
return;
}
int readCount = 0;
int keptReadCount = 0;
string header = reader.GetHeader();
BamAlignment alignment = new BamAlignment();
while (reader.GetNextAlignment(ref alignment, true))
{
readCount++;
// Flag check - Require reads to be aligned, passing filter, non-duplicate:
if (!alignment.IsMapped())
{
continue;
}
if (alignment.IsFailedQC())
{
continue;
}
if (alignment.IsDuplicate())
{
continue;
}
if (alignment.IsReverseStrand())
{
continue;
}
if (!alignment.IsMainAlignment())
{
continue;
}
// Require the alignment to start with 35 bases of non-indel:
if (alignment.CigarData[0].Type != 'M' || alignment.CigarData[0].Length < 35)
{
continue;
}
if (isPairedEnd && !alignment.IsProperPair())
{
continue;
}
int refID = alignment.RefID;
// quit if the current reference index is different from the desired reference index
if (refID != desiredRefIndex)
{
break;
}
if (refID == -1)
{
continue;
}
keptReadCount++;
if (coverageMode == CanvasCoverageMode.Binary)
{
observed.Data[alignment.Position] = 1;
}
else
{
observed.Set(alignment.Position);
}
// store fragment size, make sure it's within Int16 range and is positive (simplification for now)
if (coverageMode == CanvasCoverageMode.GCContentWeighted)
{
fragmentLengths[alignment.Position] = Convert.ToInt16(Math.Max(Math.Min(Int16.MaxValue, alignment.FragmentLength), 0));
}
}
Console.WriteLine("Kept {0} of {1} total reads", keptReadCount, readCount);
}
}
public void JumpToChromosome(string chromosomeName)
{
_bamIndexFilter = _bamReader.GetReferenceIndex(chromosomeName);
_bamReader.Jump(_bamIndexFilter, 0);
}
