private void Initialize()
{
var baseReader = new BamReader(_inputBam);
_chroms = baseReader.GetReferenceNames();
_header = baseReader.GetHeader();
_references = baseReader.GetReferences();
_header = BamStitcher.UpdateBamHeader(_header);
}
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 Process(string inputBam, string outFolder, StitcherOptions stitcherOptions)
{
var stitcher = new BamStitcher(inputBam, Path.Combine(outFolder, Path.GetFileNameWithoutExtension(inputBam) + ".stitched.bam"), stitcherOptions);
stitcher.Execute();
}