/// <summary>
/// Write out the ploidy bed file if ploidy information is available from the vcf header
/// Only create the normal XX or XY ploidy bed file so that Canvas can properly classify any abnormalities as variant.
/// If ploidy Y is > 1 produce the XY ploidy bed file, otherwise produce the XX ploidy bed file
/// </summary>
public IFileLocation CreateGermlinePloidyBed(Vcf vcf, GenomeMetadata genomeMetadata, IDirectoryLocation sampleSandbox)
{
string sexKaryotype = PloidyCorrector.GetSexChromosomeKaryotypeFromVcfHeader(vcf.VcfFile.FullName);
if (sexKaryotype == null)
{
_logger.Warn($"Sex chromosome ploidy not found in {vcf.VcfFile} header. No ploidy will be provided to Canvas.");
return(null);
}
_logger.Info($"Found sex chromosome ploidy {PloidyCorrector.PrintPloidy(sexKaryotype)} in {vcf.VcfFile}");
var ploidyInfo = new SamplePloidyInfo();
IFileLocation ploidyBed = sampleSandbox.GetFileLocation("ploidy.bed.gz");
if (sexKaryotype.ToLower().Contains("y"))
{
ploidyInfo.ProvidedPloidy = SexPloidyInfo.NormalMale;
_logger.Info($"Creating male ploidy bed file at {ploidyBed}.");
}
else
{
ploidyInfo.ProvidedPloidy = SexPloidyInfo.NormalFemale;
_logger.Info($"Creating female ploidy bed file at {ploidyBed}.");
}
string headerLine = $"{PloidyCorrector.ReferenceSexChromosomeKaryotype}={PloidyCorrector.PrettyPrintPloidy(ploidyInfo.ProvidedPloidyX.Value, ploidyInfo.ProvidedPloidyY.Value)}";
_ploidyFixer.WritePloidyBedFile(ploidyInfo, genomeMetadata, _ploidyFixer.GetParRegions(genomeMetadata),
ploidyBed.FullName, headerLine, ploidy => true);
return(ploidyBed);
}
public SpecialsController(Vcf vcf, Transform firstPersonTransform)
{
int specialsCount = vcf.Specials.Count;
_specials = new Special[specialsCount];
List <SpecialType> specialsList = vcf.Specials;
for (int i = 0; i < specialsCount; ++i)
{
_specials[i] = new Special(specialsList[i]);
}
if (firstPersonTransform != null)
{
_panel = new SpecialsPanel(firstPersonTransform);
for (int i = 0; i < MaxSpecials; ++i)
{
if (i < specialsCount)
{
_panel.TryGetSpecialSprites(specialsList[i], out _specials[i].OnSprite, out _specials[i].OffSprite);
_panel.SetSpecialHealthGroup(i, 0);
_panel.SetSpecialAmmoCount(i, _specials[i].Ammo);
}
else
{
_panel.SetSpecialHealthGroup(i, 0);
}
}
_panel.SetActiveSpecial(_activeSpecial, _specials);
}
}
/// <summary>
/// Write out the ploidy vcf file if ploidy information is available from the vcf header
/// </summary>
public Vcf CreatePloidyVcf(SampleSet <SexPloidyInfo> ploidyInfos, GenomeMetadata genomeMetadata, IDirectoryLocation sampleSandbox)
{
var ploidyVcf = new Vcf(sampleSandbox.GetFileLocation(PloidyVcfName));
_ploidyFixer.WritePloidyVcfFile(ploidyVcf, ploidyInfos, genomeMetadata);
return(ploidyVcf);
}
public CanvasSmallPedigreeOutput(
Vcf cnvVcf,
SampleSet <IntermediateOutput> intermediateOutputs)
{
CnvVcf = cnvVcf;
IntermediateOutputs = intermediateOutputs;
}
public CanvasTumorNormalWgsInput(Bam tumorBam, Bam normalBam, Vcf normalVcf, Vcf somaticVcf, GenomeMetadata genomeMetadata)
{
TumorBam = tumorBam;
NormalBam = normalBam;
NormalVcf = normalVcf;
SomaticVcf = somaticVcf;
GenomeMetadata = genomeMetadata;
}
public CanvasTumorNormalWgsInput(Bam tumorBam, Bam normalBam, Vcf normalVcf, Vcf somaticVcf, GenomeMetadata genomeMetadata, SexPloidyInfo sexPloidy)
{
TumorBam = tumorBam;
NormalBam = normalBam;
NormalVcf = normalVcf;
SomaticVcf = somaticVcf;
GenomeMetadata = genomeMetadata;
SexPloidy = sexPloidy;
}
public static Vcf ParseVcf(string filename)
{
var vcf = new Vcf();
using (var br = new Bwd2Reader(filename))
{
br.FindNext("VCFC");
vcf.VariantName = br.ReadCString(16);
vcf.VdfFilename = br.ReadCString(13);
vcf.VtfFilename = br.ReadCString(13);
vcf.EngineType = br.ReadUInt32();
vcf.SuspensionType = br.ReadUInt32();
vcf.BrakesType = br.ReadUInt32();
vcf.WdfFrontFilename = br.ReadCString(13);
vcf.WdfMidFilename = br.ReadCString(13);
vcf.WdfBackFilename = br.ReadCString(13);
vcf.ArmorFront = br.ReadUInt32();
vcf.ArmorLeft = br.ReadUInt32();
vcf.ArmorRight = br.ReadUInt32();
vcf.ArmorRear = br.ReadUInt32();
vcf.ChassisFront = br.ReadUInt32();
vcf.ChassisLeft = br.ReadUInt32();
vcf.ChassisRight = br.ReadUInt32();
vcf.ChassisRear = br.ReadUInt32();
vcf.ArmorOrChassisLeftToAdd = br.ReadUInt32();
br.FindNext("WEPN");
vcf.Weapons = new List <VcfWeapon>();
while (br.Current != null && br.Current.Name != "EXIT")
{
var vcfWeapon = new VcfWeapon
{
MountPoint = (MountPoint)br.ReadUInt32(),
GdfFilename = br.ReadCString(13)
};
vcf.Weapons.Add(vcfWeapon);
br.Next();
}
}
if (vcf.WdfFrontFilename.ToUpper() != "NULL")
{
vcf.FrontWheelDef = WdfParser.ParseWdf(vcf.WdfFrontFilename);
}
if (vcf.WdfMidFilename.ToUpper() != "NULL")
{
vcf.MidWheelDef = WdfParser.ParseWdf(vcf.WdfMidFilename);
}
if (vcf.WdfBackFilename.ToUpper() != "NULL")
{
vcf.BackWheelDef = WdfParser.ParseWdf(vcf.WdfBackFilename);
}
return(vcf);
}
public static CanvasOutput GetFromStub(IFileLocation stub)
{
Vcf cnvVcf = Vcf.GetVcfFromStub(stub);
IFileLocation coverageAndVariantFrequencies = stub.AppendName(".CoverageAndVariantFrequency.txt");
IFileLocation variantFrequencies = stub.AppendName(".VFResults.txt.gz");
IFileLocation variantFrequenciesBaf = stub.AppendName(".VFResults.baf");
IFileLocation partitioned = stub.AppendName(".partitioned");
return(new CanvasOutput(cnvVcf, coverageAndVariantFrequencies, variantFrequencies,
variantFrequenciesBaf, partitioned));
}
private CanvasOutput GetCanvasOutput(string sampleId, IDirectoryLocation sampleSandbox)
{
var cnvVcf = new Vcf(sampleSandbox.GetFileLocation("CNV.vcf.gz"));
var tempCnvDirectory = sampleSandbox.GetDirectoryLocation($"TempCNV_{sampleId}");
var variantFrequencies = tempCnvDirectory.GetFileLocation($"VFResults{sampleId}.txt.gz");
var variantFrequenciesBaf = tempCnvDirectory.GetFileLocation($"VFResults{sampleId}.txt.gz.baf");
IFileLocation coverageAndVariantFrequencies = sampleSandbox.GetFileLocation("CNV.CoverageAndVariantFrequency.txt");
IFileLocation tempStub = tempCnvDirectory.GetFileLocation($"{sampleId}");
IFileLocation partitioned = tempStub.AppendName(".partitioned");
return(new CanvasOutput(cnvVcf, coverageAndVariantFrequencies, variantFrequencies,
variantFrequenciesBaf, partitioned));
}
public IntermediateOutput(Vcf cnvVcf, IFileLocation coverageAndVariantFrequencies, IFileLocation variantFrequencies, IFileLocation variantFrequenciesBaf,
IFileLocation partitioned, IFileLocation coverageBigwig, BgzfFile bAlleleBedgraph, BgzfFile copyNumberBedgraph)
{
CnvVcf = cnvVcf;
#pragma warning disable CS0618 // Type or member is obsolete
CoverageAndVariantFrequencies = coverageAndVariantFrequencies;
VariantFrequencies = variantFrequencies;
VariantFrequenciesBaf = variantFrequenciesBaf;
Partitioned = partitioned;
#pragma warning restore CS0618 // Type or member is obsolete
CoverageBigwig = coverageBigwig;
BAlleleBedgraph = bAlleleBedgraph;
CopyNumberBedgraph = copyNumberBedgraph;
}
public CanvasTumorNormalEnrichmentInput(
Bam tumorBam,
Bam normalBam,
Vcf normalVcf,
Vcf somaticVcf,
GenomeMetadata genomeMetadata,
NexteraManifest nexteraManifest)
{
TumorBam = tumorBam;
NormalBam = normalBam;
NormalVcf = normalVcf;
SomaticVcf = somaticVcf;
GenomeMetadata = genomeMetadata;
NexteraManifest = nexteraManifest;
}
private CanvasSmallPedigreeOutput GetCanvasOutput(SampleSet <Bam> pedigreeBams, IDirectoryLocation sampleSandbox)
{
var readGroupSamples = pedigreeBams.SelectData(GetReadGroupSample);
var intermediateResults = readGroupSamples.SelectData(readGroupSample =>
{
var variantFrequencies = SingleSampleCallset.GetVfSummaryPath(sampleSandbox, readGroupSample);
var variantFrequenciesBaf = SingleSampleCallset.GetVfSummaryBafPath(sampleSandbox, readGroupSample);
var partitioned = SingleSampleCallset.GetPartitionedPath(sampleSandbox, readGroupSample);
var coverageAndVariantFrequencies = SingleSampleCallset.GetCoverageAndVariantFrequencyOutput(sampleSandbox, readGroupSample);
return(new IntermediateOutput(coverageAndVariantFrequencies, variantFrequencies, variantFrequenciesBaf, partitioned));
});
var cnvVcf = new Vcf(sampleSandbox.GetFileLocation("CNV.vcf.gz"));
return(new CanvasSmallPedigreeOutput(cnvVcf, intermediateResults));
}
public CanvasOutput(
Vcf cnvVcf,
IFileLocation coverageAndVariantFrequencies,
IFileLocation variantFrequencies = null,
IFileLocation variantFrequenciesBaf = null,
IFileLocation partitioned = null,
IFileLocation binSize = null,
IFileLocation normalBinned = null)
{
CnvVcf = cnvVcf;
CoverageAndVariantFrequencies = coverageAndVariantFrequencies;
VariantFrequencies = variantFrequencies;
VariantFrequenciesBaf = variantFrequenciesBaf;
Partitioned = partitioned;
}
/// <summary>
/// Write out the ploidy bed file if ploidy information is available from the vcf header
/// </summary>
public IFileLocation CreatePloidyBed(Vcf vcf, GenomeMetadata genomeMetadata, IDirectoryLocation sampleSandbox)
{
IFileLocation ploidyBed = sampleSandbox.GetFileLocation("ploidy.bed.gz");
string fastaPath = genomeMetadata.Sequences.First().FastaPath;
if (_ploidyFixer.GeneratePloidyBedFileFromVcf(
genomeMetadata,
fastaPath,
vcf.VcfFile.FullName,
ploidyBed.FullName, sampleSandbox.FullName, _logger, _workManager))
{
return(ploidyBed);
}
_logger.Warn($"Sex chromosome ploidy not found in {vcf.VcfFile} header. No ploidy will be provided to Canvas.");
return(null);
}
private CanvasSmallPedigreeOutput GetCanvasOutput(SampleSet <CanvasPedigreeSample> pedigreeSamples, IDirectoryLocation sampleSandbox)
{
var intermediateResults = pedigreeSamples.SelectSamples(sampleInfo =>
{
var sampleId = sampleInfo.Id;
var variantFrequencies = SingleSampleCallset.GetVfSummaryPath(sampleSandbox, sampleId);
var variantFrequenciesBaf = SingleSampleCallset.GetVfSummaryBafPath(sampleSandbox, sampleId);
var partitioned = SingleSampleCallset.GetPartitionedPath(sampleSandbox, sampleId);
var coverageAndVariantFrequencies = SingleSampleCallset.GetCoverageAndVariantFrequencyOutput(sampleSandbox, sampleId);
var singleSampleVcf = SingleSampleCallset.GetVcfOutput(sampleSandbox, sampleId);
var coverageBigwig = SingleSampleCallset.GetCoverageBigWig(sampleSandbox, sampleId);
var bAlleleBedgraph = SingleSampleCallset.GetBAlleleBedGraph(sampleSandbox, sampleId);
var copyNumberBedgraph = SingleSampleCallset.GetCopyNumberBedGraph(sampleSandbox, sampleId);
return(new IntermediateOutput(new Vcf(singleSampleVcf), coverageAndVariantFrequencies, variantFrequencies, variantFrequenciesBaf,
partitioned, coverageBigwig, bAlleleBedgraph, copyNumberBedgraph));
});
var cnvVcf = new Vcf(sampleSandbox.GetFileLocation("CNV.vcf.gz"));
return(new CanvasSmallPedigreeOutput(cnvVcf, intermediateResults));
}
private CanvasEnrichmentOutput GetCanvasOutput(string sampleId, IDirectoryLocation sampleSandbox)
{
var cnvVcf = new Vcf(sampleSandbox.GetFileLocation("CNV.vcf.gz"));
var tempCnvDirectory = sampleSandbox.GetDirectoryLocation($"TempCNV_{sampleId}");
var variantFrequencies = tempCnvDirectory.GetFileLocation($"VFResults{sampleId}.txt.gz");
var variantFrequenciesBaf = tempCnvDirectory.GetFileLocation($"VFResults{sampleId}.txt.gz.baf");
IFileLocation coverageAndVariantFrequencies = sampleSandbox.GetFileLocation("CNV.CoverageAndVariantFrequency.txt");
IFileLocation tempStub = tempCnvDirectory.GetFileLocation($"{sampleId}");
IFileLocation partitioned = tempStub.AppendName(".partitioned");
var canvasOutput = new CanvasOutput(cnvVcf, coverageAndVariantFrequencies, variantFrequencies,
variantFrequenciesBaf, partitioned);
IFileLocation binSize = tempStub.AppendName(".binsize");
IFileLocation normalBinned = tempStub.AppendName(".normal.binned");
IFileLocation unsmoothedCnd = tempStub.AppendName(".ratio.binned.cnd");
if (!binSize.Exists)
{
binSize = null;
}
return(new CanvasEnrichmentOutput(canvasOutput, binSize, normalBinned, unsmoothedCnd));
}
private CanvasSmallPedigreeOutput Load(CanvasSmallPedigreeInput input)
{
var intermediateOutputs = input.Samples.SelectData((info, sample) =>
{
var stub = GetSingleSampleOutputStub(info);
var coverageAndVariantFrequency = SingleSampleCallset.GetCoverageAndVariantFrequencyOutput(stub);
var singleSampleVcf = new Vcf(SingleSampleCallset.GetVcfOutput(stub));
var partitioned = SingleSampleCallset.GetPartitionedPath(stub);
var variantFrequencies = SingleSampleCallset.GetVfSummaryPath(stub);
var variantFrequenciesBaf = SingleSampleCallset.GetVfSummaryBafPath(stub);
var coverageBigwig = SingleSampleCallset.GetCoverageBigWig(stub);
var bAlleleBedgraph = SingleSampleCallset.GetBAlleleBedGraph(stub);
var copyNumberBedgraph = SingleSampleCallset.GetCopyNumberBedGraph(stub);
return(new IntermediateOutput(singleSampleVcf, coverageAndVariantFrequency, variantFrequencies, variantFrequenciesBaf, partitioned,
coverageBigwig, bAlleleBedgraph, copyNumberBedgraph));
});
return(new CanvasSmallPedigreeOutput(new Vcf(GetPedigreeVcf()), intermediateOutputs));
}
public void Configure(Vdf vdf, Vcf vcf)
{
Vdf = vdf;
Vcf = vcf;
_vehicleHealthGroups = Vdf.PartsThirdPerson.Count;
int systemCount = (int)SystemType.TotalSystems;
_vehicleHitPoints = new int[systemCount];
_vehicleStartHitPoints = new int[systemCount];
_vehicleStartHitPoints[(int)SystemType.Vehicle] = VehicleStartHealth;
_vehicleStartHitPoints[(int)SystemType.Suspension] = CoreStartHealth;
_vehicleStartHitPoints[(int)SystemType.Brakes] = CoreStartHealth;
_vehicleStartHitPoints[(int)SystemType.Engine] = CoreStartHealth;
_vehicleStartHitPoints[(int)SystemType.FrontArmor] = (int)vcf.ArmorFront;
_vehicleStartHitPoints[(int)SystemType.RightArmor] = (int)vcf.ArmorRight;
_vehicleStartHitPoints[(int)SystemType.BackArmor] = (int)vcf.ArmorRear;
_vehicleStartHitPoints[(int)SystemType.LeftArmor] = (int)vcf.ArmorLeft;
_vehicleStartHitPoints[(int)SystemType.FrontChassis] = (int)vcf.ChassisFront;
_vehicleStartHitPoints[(int)SystemType.RightChassis] = (int)vcf.ChassisRight;
_vehicleStartHitPoints[(int)SystemType.BackChassis] = (int)vcf.ChassisRear;
_vehicleStartHitPoints[(int)SystemType.LeftChassis] = (int)vcf.ChassisLeft;
_vehicleStartHitPoints[(int)SystemType.TireFL] = TireStartHealth;
_vehicleStartHitPoints[(int)SystemType.TireFR] = TireStartHealth;
_vehicleStartHitPoints[(int)SystemType.TireBL] = TireStartHealth;
_vehicleStartHitPoints[(int)SystemType.TireBR] = TireStartHealth;
for (int i = 0; i < systemCount; ++i)
{
_vehicleHitPoints[i] = _vehicleStartHitPoints[i];
}
}
public CanvasSmallPedigreeInput(GenomeMetadata genomeMetadata, SampleSet <CanvasPedigreeSample> samples, Vcf vcf)
{
GenomeMetadata = genomeMetadata;
Samples = samples;
Vcf = vcf;
}
public GameObject ImportVcf(string filename, bool importFirstPerson, out Vdf vdf)
{
Vcf vcf = VcfParser.ParseVcf(filename);
vdf = VdfParser.ParseVdf(vcf.VdfFilename);
Vtf vtf = VtfParser.ParseVtf(vcf.VtfFilename);
Car carObject = Object.Instantiate(_carPrefab);
carObject.Configure(vdf, vcf);
carObject.gameObject.name = vdf.Name + " (" + vcf.VariantName + ")";
foreach (VLoc vLoc in vdf.VLocs)
{
GameObject vlocGo = new GameObject("VLOC");
vlocGo.transform.parent = carObject.transform;
vlocGo.transform.localRotation = Quaternion.LookRotation(vLoc.Forward, vLoc.Up);
vlocGo.transform.localPosition = vLoc.Position;
}
GameObject chassis = new GameObject("Chassis");
chassis.transform.parent = carObject.transform;
GameObject thirdPerson = new GameObject("ThirdPerson");
thirdPerson.transform.parent = chassis.transform;
Transform[] weaponMountTransforms = new Transform[vdf.HLocs.Count];
for (int i = 0; i < vdf.HLocs.Count; ++i)
{
HLoc hloc = vdf.HLocs[i];
Transform mountPoint = new GameObject(hloc.Label).transform;
mountPoint.parent = thirdPerson.transform;
mountPoint.localRotation = Quaternion.LookRotation(hloc.Forward, hloc.Up);
mountPoint.localPosition = hloc.Position;
weaponMountTransforms[i] = mountPoint;
}
Dictionary <string, GameObject> partDict = new Dictionary <string, GameObject>();
for (int i = 0; i < vdf.PartsThirdPerson.Count; ++i)
{
GameObject healthObject = new GameObject("Health " + i);
healthObject.transform.SetParent(thirdPerson.transform);
ImportCarParts(partDict, healthObject, vtf, vdf.PartsThirdPerson[i], _noColliderPrefab, false, false, i);
if (i != 0)
{
healthObject.SetActive(false);
}
}
MeshFilter[] meshFilters = thirdPerson.GetComponentsInChildren <MeshFilter>();
Bounds bounds = new Bounds();
bounds.SetMinMax(Vector3.one * float.MaxValue, Vector3.one * float.MinValue);
foreach (MeshFilter meshFilter in meshFilters)
{
Vector3 min = Vector3.Min(bounds.min, meshFilter.transform.position + meshFilter.sharedMesh.bounds.min) - thirdPerson.transform.position;
Vector3 max = Vector3.Max(bounds.max, meshFilter.transform.position + meshFilter.sharedMesh.bounds.max) - thirdPerson.transform.position;
bounds.SetMinMax(min, max);
}
GameObject chassisCollider = new GameObject("ChassisColliders");
chassisCollider.transform.parent = carObject.transform;
ImportCarParts(partDict, chassisCollider, vtf, vdf.PartsThirdPerson[0], _carBodyPrefab, true);
for (int i = 0; i < vcf.Weapons.Count; ++i)
{
VcfWeapon weapon = vcf.Weapons[i];
int mountPoint = weapon.MountPoint;
HLoc hloc = vdf.HLocs[mountPoint];
weapon.RearFacing = hloc.FacingDirection == 2;
SdfPart[] partsArray;
switch (hloc.MeshType)
{
case HardpointMeshType.Top:
partsArray = weapon.Gdf.TopParts;
break;
case HardpointMeshType.Side:
partsArray = weapon.Gdf.SideParts;
break;
case HardpointMeshType.Inside:
partsArray = weapon.Gdf.InsideParts;
break;
case HardpointMeshType.Turret:
partsArray = weapon.Gdf.TurretParts;
break;
default:
partsArray = null;
break;
}
if (partsArray != null)
{
Transform weaponTransform = new GameObject(weapon.Gdf.Name).transform;
weaponTransform.SetParent(weaponMountTransforms[i]);
weaponTransform.localPosition = Vector3.zero;
weaponTransform.localRotation = Quaternion.identity;
ImportCarParts(partDict, weaponTransform.gameObject, vtf, partsArray, _noColliderPrefab, false);
weapon.Transform = weaponTransform;
// Disable depth test for 'inside' weapons, otherwise they are obscured.
if (hloc.MeshType == HardpointMeshType.Inside)
{
MeshRenderer weaponRenderer = weaponTransform.GetComponentInChildren <MeshRenderer>();
if (weaponRenderer != null)
{
weaponRenderer.sharedMaterial.shader = Shader.Find("Custom/CutOutWithoutZ");
}
}
}
else
{
weapon.Transform = chassis.transform;
}
}
// Note: The following is probably how I76 does collision detection. Two large boxes that encapsulate the entire vehicle.
// Right now this won't work with Open76's raycast suspension, so I'm leaving this off for now. Investigate in the future.
//var innerBox = chassisCollider.AddComponent<BoxCollider>();
//innerBox.center = vdf.BoundsInner.center;
//innerBox.size = vdf.BoundsInner.size;
//var outerBox = chassisCollider.AddComponent<BoxCollider>();
//outerBox.center = vdf.BoundsOuter.center;
//outerBox.size = vdf.BoundsOuter.size;
RaySusp[] frontWheels = null;
if (vcf.FrontWheelDef != null)
{
frontWheels = CreateWheelPair(partDict, "Front", 0, carObject.gameObject, vdf, vtf, vcf.FrontWheelDef);
carObject.Movement.FrontWheels = frontWheels;
}
if (vcf.MidWheelDef != null)
{
CreateWheelPair(partDict, "Mid", 2, carObject.gameObject, vdf, vtf, vcf.MidWheelDef);
}
RaySusp[] rearWheels = null;
if (vcf.BackWheelDef != null)
{
rearWheels = CreateWheelPair(partDict, "Back", 4, carObject.gameObject, vdf, vtf, vcf.BackWheelDef);
carObject.Movement.RearWheels = rearWheels;
}
if (importFirstPerson)
{
GameObject firstPerson = new GameObject("FirstPerson");
firstPerson.transform.parent = chassis.transform;
ImportCarParts(partDict, firstPerson, vtf, vdf.PartsFirstPerson, _noColliderPrefab, false, true, 0, LayerMask.NameToLayer("FirstPerson"));
carObject.InitPanels();
firstPerson.SetActive(false);
}
carObject.Movement.Initialise(chassis.transform, frontWheels, rearWheels);
return(carObject.gameObject);
}
public StringBuilder GetMultiSampleCommandLine(SampleSet <CanvasPedigreeSample> samples, GenomeMetadata genomeMetadata, Vcf vcf, IDirectoryLocation sampleSandbox)
{
StringBuilder commandLine = new StringBuilder();
foreach (var sampleKvp in samples)
{
var sampleId = sampleKvp.Key.Id;
var sample = sampleKvp.Value;
commandLine.Append($" --bam \"{sample.Bam.BamFile}\"");
if (sample.SampleType != SampleType.Other)
{
commandLine.Append($" --{sample.SampleType.GetOptionName()} {sampleId}");
}
}
IFileLocation kmerFasta = _annotationFileProvider.GetKmerFasta(genomeMetadata);
commandLine.Append($" --reference \"{kmerFasta}\"");
IDirectoryLocation wholeGenomeFasta = new FileLocation(genomeMetadata.Sequences.First().FastaPath).Directory;
commandLine.Append($" --genome-folder \"{wholeGenomeFasta}\"");
IFileLocation filterBed = _annotationFileProvider.GetFilterBed(genomeMetadata);
commandLine.Append($" --filter-bed \"{filterBed}\"");
commandLine.Append($" --output \"{sampleSandbox}\"");
return(commandLine);
}
public CanvasResequencingInput(Bam bam, Vcf vcf, GenomeMetadata genomeMetadata)
{
Bam = bam;
GenomeMetadata = genomeMetadata;
Vcf = vcf;
}
public WeaponsController(Car car, Vcf vcf, Transform firstPersonTransform)
{
_car = car;
int weaponCount = vcf.Weapons.Count;
_weapons = new Weapon[weaponCount];
_weaponAudio = car.gameObject.AddComponent <AudioSource>();
_weaponAudio.volume = 0.5f;
_weaponEmptySound = CacheManager.Instance.GetAudioClip("cammo.gpw");
_weaponBrokenSound = CacheManager.Instance.GetAudioClip("cwstat.gpw");
_firingWeapons = new List <Weapon>(5);
_weaponGroups = new List <int>();
List <VcfWeapon> weaponsList = vcf.Weapons;
weaponsList.Sort((x, y) =>
{
int compare = x.RearFacing.CompareTo(y.RearFacing);
if (compare != 0)
{
return(compare);
}
return(x.Gdf.WeaponGroup.CompareTo(y.Gdf.WeaponGroup));
});
int seperatorIndex = -1;
for (int i = 0; i < weaponCount; ++i)
{
AudioClip fireSound = CacheManager.Instance.GetAudioClip(weaponsList[i].Gdf.SoundName);
_weapons[i] = new Weapon(weaponsList[i].Gdf, weaponsList[i].Transform)
{
FireSound = fireSound,
RearFacing = weaponsList[i].RearFacing,
Index = i
};
if (_weapons[i].RearFacing)
{
if (seperatorIndex == -1)
{
seperatorIndex = i;
}
_weapons[i].WeaponGroupOffset += 100;
}
if (!_weaponGroups.Contains(_weapons[i].WeaponGroupOffset))
{
_weaponGroups.Add(_weapons[i].WeaponGroupOffset);
}
}
if (firstPersonTransform != null)
{
_panel = new WeaponsPanel(firstPersonTransform);
_panel.SetWeaponCount(weaponCount);
for (int i = 0; i < weaponCount; ++i)
{
_panel.SetWeaponHealthGroup(i, 0);
_panel.SetWeaponAmmoCount(i, _weapons[i].Ammo);
_panel.TryGetWeaponSprites(weaponsList[i].Gdf, out _weapons[i].OnSprite, out _weapons[i].OffSprite);
}
if (seperatorIndex != -1)
{
_panel.SeparatorIndex = seperatorIndex;
}
if (_weaponGroups.Count > 0)
{
_panel.UpdateActiveWeaponGroup(_weaponGroups[_activeGroup], _weapons);
}
}
}
public StringBuilder GetMultiSampleCommandLine(SampleSet <CanvasPedigreeSample> samples, GenomeMetadata genomeMetadata, Vcf vcf, IDirectoryLocation sampleSandbox)
{
StringBuilder commandLine = new StringBuilder();
// move proband to the front of collection (enum Proband gets the lowest int value )
var sortedBySampleTypeSamples = samples.OrderBy(sample => sample.Value.SampleType);
foreach (var sampleKvp in sortedBySampleTypeSamples)
{
var sampleId = sampleKvp.Key.Id;
var sample = sampleKvp.Value;
commandLine.Append($" --bam \"{sample.Bam.BamFile}\" {sample.SampleType} {sampleId}");
}
IFileLocation kmerFasta = _annotationFileProvider.GetKmerFasta(genomeMetadata);
commandLine.Append($" --reference \"{kmerFasta}\"");
IDirectoryLocation wholeGenomeFasta = new FileLocation(genomeMetadata.Contigs().First().FastaPath).Directory;
commandLine.Append($" --genome-folder \"{wholeGenomeFasta}\"");
IFileLocation filterBed = _annotationFileProvider.GetFilterBed(genomeMetadata);
commandLine.Append($" --filter-bed \"{filterBed}\"");
commandLine.Append($" --output \"{sampleSandbox}\"");
return(commandLine);
}
