private void FlushBufferedRecords(ReadsForPosition reads)
{
foreach (byte[] buffer in reads.Reads)
{
_bamWriter.WriteAlignment(buffer);
}
}
private void AdjustMates(string tmpFile, BamWriter writer)
{
// Second pass: Adjust flags on mates
Logger.WriteToLog("Writing reads with corrected mate flags, {0} total remapped reads", _remappings.Count);
var read = new BamAlignment();
using (var reader = new BamReader(tmpFile))
{
while (true)
{
var result = reader.GetNextAlignment(ref read, false);
if (!result)
{
break;
}
// Adjust flags as needed:
var mateKey = string.Format("{0}-{1}", read.Name, read.IsFirstMate() ? 2 : 1);
RemapInfo info;
if (!_remappings.TryGetValue(mateKey, out info))
{
writer.WriteAlignment(read);
continue;
}
if (info.Start == -1)
{
read.SetIsMateUnmapped(true);
read.SetIsProperPair(false);
read.FragmentLength = 0;
}
else
{
read.MatePosition = info.Start;
}
if (read.IsMateMapped() && read.IsProperPair())
{
int readEnd = read.Position + (int)read.CigarData.GetReferenceSpan() - 1;
// todo jg - should FragmentLength be 0 if the reads are mapped to diff chrs
read.FragmentLength = (read.Position < info.Start
? info.End - read.Position + 1
: info.Start - readEnd - 1);
}
writer.WriteAlignment(read);
}
}
}
public void WriteAlignment(BamAlignment alignment)
{
if (alignment == null)
{
_writer?.Dispose();
}
else
{
_writer.WriteAlignment(alignment);
}
}
public void Process(string inputBam, string outFolder, StitcherOptions stitcherOptions)
{
var jobManager = new JobManager(10);
var jobs = new List <IJob>();
var perChromBams = new List <string>();
// Process each of the chromosomes separately
foreach (var chrom in _chroms)
{
var intermediateOutput = Path.Combine(outFolder, Path.GetFileNameWithoutExtension(inputBam) + "." + chrom + ".stitched.bam");
perChromBams.Add(intermediateOutput);
var stitcher = new BamStitcher(inputBam, intermediateOutput, stitcherOptions, chrFilter: chrom);
jobs.Add(new GenericJob(() => stitcher.Execute(), "Stitcher_" + chrom));
}
jobManager.Process(jobs);
// Combine the per-chromosome bams
Logger.WriteToLog("Writing final bam.");
var outputBam = Path.Combine(outFolder, Path.GetFileNameWithoutExtension(inputBam) + ".final.stitched.bam");
using (var finalOutput = new BamWriter(outputBam, _header, _references))
{
foreach (var bam in perChromBams)
{
Logger.WriteToLog("Adding " + bam + " to final bam.");
var bamAlignment = new BamAlignment();
using (var bamReader = new BamReader(bam))
{
while (true)
{
var hasMoreReads = bamReader.GetNextAlignment(ref bamAlignment, false);
if (!hasMoreReads)
{
break;
}
finalOutput.WriteAlignment(bamAlignment);
}
}
File.Delete(bam);
}
}
Logger.WriteToLog("Finished combining per-chromosome bams into final bam at " + outputBam);
}
public void HappyPath()
{
//var bamFilePath = Path.Combine(TestPaths.SharedBamDirectory, "Chr17Chr19.bam");
//Assert.True(File.Exists(bamFilePath));
// TODO figure out how to access the shared bams
var tempPath = $"TemporaryBamFile_{Guid.NewGuid()}.bam";
if (File.Exists(tempPath))
{
File.Delete(tempPath);
}
using (var bamWriter = new BamWriter(tempPath, "header", new List <GenomeMetadata.SequenceMetadata>()))
{
bamWriter.WriteAlignment(TestHelpers.CreateBamAlignment("ATCG", 1, 10, 30, true));
}
var bamWriterFactory = new BamWriterFactory(1, tempPath);
var tempPath2 = $"TemporaryBamFile_{Guid.NewGuid()}.bam";
if (File.Exists(tempPath2))
{
File.Delete(tempPath2);
}
var bamWriterHandle = bamWriterFactory.CreateSingleBamWriter(tempPath2);
bamWriterHandle.WriteAlignment(TestHelpers.CreateBamAlignment("ATCAG", 1, 10, 30, true));
bamWriterHandle.WriteAlignment(null);
using (var reader = new BamReader(tempPath2))
{
// TODO more specific?
var header = reader.GetHeader();
Assert.Contains("ID:Gemini", header);
Assert.Contains("PN:Gemini", header);
}
File.Delete(tempPath);
File.Delete(tempPath2);
}
/// <summary>
/// Seek to the unaligned (and mate-unaligned) reads at the tail of the input file, and write them all out to the output file.
/// </summary>
private void WriteUnalignedReads(BamWriter writer)
{
Logger.WriteToLog("Writing unaligned reads");
using (var reader = new BamReader(_inputFile))
{
reader.JumpToUnaligned();
var read = new BamAlignment();
while (true)
{
var result = reader.GetNextAlignment(ref read, false);
if (!result)
{
break;
}
if (read.RefID != -1)
{
continue; // skip over last reads
}
writer.WriteAlignment(read);
}
}
}
public void WriteAlignment(BamAlignment alignment)
{
_writer.WriteAlignment(alignment);
}
