private static void MergeAndFinalizeBam(List <string> perChromPaths, ISamtoolsWrapper samtoolsWrapper, string outFolder, string outputBamName)
{
var finalBams = perChromPaths;
var mergedBam = Path.Combine(outFolder, outputBamName);
Logger.WriteToLog($"Calling samtools cat on {perChromPaths.Count} files to create {mergedBam}.");
samtoolsWrapper.SamtoolsCat(mergedBam, finalBams);
Logger.WriteToLog($"Calling samtools index on {mergedBam}.");
samtoolsWrapper.SamtoolsIndex(mergedBam);
Logger.WriteToLog("Done finalizing bam.");
}
private static string MergeAndFinalizeBam(List <string> finalBams, ISamtoolsWrapper samtoolsWrapper, string outFolder, string outFileName, bool keepUnmerged = false, bool doIndex = false, bool doSort = true)
{
var mergedBam = Path.Combine(outFolder, outFileName);
var sortedMerged = mergedBam + ".sorted";
var sortedMergedFinal = sortedMerged + ".bam";
Logger.WriteToLog($"Calling cat on {finalBams.Count} with output at {mergedBam}.");
foreach (var finalBam in finalBams)
{
Logger.WriteToLog($"Intermediate bam: {finalBam}\t{new FileInfo(finalBam).Length}B");
}
samtoolsWrapper.SamtoolsCat(mergedBam, finalBams);
if (doSort)
{
Logger.WriteToLog($"Calling samtools sort on {mergedBam}.");
samtoolsWrapper.SamtoolsSort(mergedBam, sortedMerged, 3, 500);
}
if (doIndex)
{
Logger.WriteToLog($"Calling samtools index on {sortedMergedFinal}.");
samtoolsWrapper.SamtoolsIndex(sortedMergedFinal);
}
Logger.WriteToLog("Done finalizing bam.");
if (File.Exists(sortedMergedFinal) && !keepUnmerged)
{
Logger.WriteToLog("Deleting intermediate bams.");
foreach (var finalBam in finalBams)
{
File.Delete(finalBam);
}
File.Delete(mergedBam);
Logger.WriteToLog("Finished deleting intermediate bams.");
}
return(sortedMergedFinal);
}