public BamStitcher(string inBam, string outBam, StitcherOptions options, string chrFilter = null)
{
_inBam = inBam;
_outBam = outBam;
_options = options;
_chrFilter = chrFilter;
}
public ApplicationOptions(string[] args)
{
StitcherOptions = new StitcherOptions();
var options = new OptionSet
{
{ "Bam=", "{PATH} to the original bam file. (Required).", o => InputBam = o },
{ "OutFolder=", "{PATH} of directory in which to create the new bam file. (Required).", o => OutFolder = o },
{ "MinBaseCallQuality=", "{INT} cutoff for which, in case of a stitching conflict, bases with qscore less than this value will automatically be disregarded in favor of the mate's bases.", o => StitcherOptions.MinBaseCallQuality = int.Parse(o) },
{ "FilterMinMapQuality=", "{INT} indicating reads with map quality less than this value should be filtered. Default: 20.", o => StitcherOptions.FilterMinMapQuality = int.Parse(o) },
{ "FilterDuplicates=", "{BOOL} indicating whether reads marked as duplicates shall be filtered. Default: true.", o => StitcherOptions.FilterDuplicates = bool.Parse(o) },
{ "FilterForProperPairs=", "{BOOL} indicating whether reads marked as not proper pairs shall be filtered. Default: false.", o => StitcherOptions.FilterForProperPairs = bool.Parse(o) },
{ "FilterUnstitchablePairs=", "{BOOL} indicating whether read pairs with incompatible CIGAR strings shall be filtered. Default: false.", o => StitcherOptions.FilterUnstitchablePairs = bool.Parse(o) },
{ "NifyUnstitchablePairs=", "{BOOL} indicating whether read pairs with incompatible CIGAR strings shall be N-ified. Default: true.", o => StitcherOptions.NifyUnstitchablePairs = bool.Parse(o) },
{ "StitchGappedPairs=", "{BOOL} indicating whehter read pairs with no overlap shall still be conceptually 'stitched'. "
+ "While there will be no bases in the stitched section, the forward and reverse segments shall still be linked"
+ "and variants in them might be phased downstream. Default: false.", o => StitcherOptions.StitchGappedPairs = bool.Parse(o) },
{ "UseSoftClippedBases=", "{BOOL} indicating whether we should allow bases softclipped from the (non-probe) ends of reads to inform stitching. Default: true.", o => StitcherOptions.UseSoftClippedBases = bool.Parse(o) },
{ "IdentifyDuplicates=", "{BOOL} indicating whether we should check each alignment's position and sequence to see if it is a duplicate (rather than trusting the flags). Default: false.", o => StitcherOptions.IdentifyDuplicates = bool.Parse(o) },
{ "NifyDisagreement=", "{BOOL} indicating whether or not to turn high-quality disagreeing overlap bases to Ns. Default: false.", o => StitcherOptions.NifyDisagreements = bool.Parse(o) },
{ "Debug=", "{BOOL} indicating whether we should run in debug (verbose) mode. Default: false.", o => StitcherOptions.Debug = bool.Parse(o) },
{ "LogFileName=", "{STRING} Name for stitcher log file. Default: StitcherLog.txt.", o => StitcherOptions.LogFileName = o.Trim() },
{ "ThreadByChr=", "{BOOL} Whether to thread by chromosome (beta). Default: false.", o => StitcherOptions.ThreadByChromosome = bool.Parse(o) },
{ "DebugSummary=", "{BOOL} indicating whether we should run in debug (verbose) mode. Default: false.", o => StitcherOptions.DebugSummary = bool.Parse(o) },
{ "StitchProbeSoftclips=", "{BOOL} indicating whether to allow probe softclips that overlap the mate to contribute to a stitched direction. Default: false.", o => StitcherOptions.StitchProbeSoftclips = bool.Parse(o) },
{ "MaxReadLength=", "{INT} indicating the maximum expected length of individual reads, used to determine the maximum expected stitched read length (2*len - 1). For optimal performance, set as low as appropriate (i.e. the actual single-read length) for your data. Default: 1024.", o => StitcherOptions.MaxReadLength = int.Parse(o) },
{ "v|ver", "displays the version", o => ShowVersion = o != null }
};
options.Parse(args);
OptionSet = options;
}
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();
}
public StitcherApplicationOptions()
{
StitcherOptions = new StitcherOptions();
}
