void init()
{
workunitWriteLimit = getOptInt(THOROPT_OUTPUTLIMIT, DEFAULT_WUIDWRITE_LIMIT);
if (workunitWriteLimit>DALI_RESULT_OUTPUTMAX)
throw MakeActivityException(this, 0, "Dali result outputs are restricted to a maximum of %d MB, the default limit is %d MB. A huge dali result usually indicates the ECL needs altering.", DALI_RESULT_OUTPUTMAX, DEFAULT_WUIDWRITE_LIMIT);
assertex(workunitWriteLimit<=0x1000); // 32bit limit because MemoryBuffer/CMessageBuffers involved etc.
workunitWriteLimit *= 0x100000;
}
virtual void init()
{
CMasterActivity::init();
workunitWriteLimit = activityMaxSize ? activityMaxSize : getOptInt(THOROPT_OUTPUTLIMIT, DEFAULT_WUIDWRITE_LIMIT);
if (workunitWriteLimit>DALI_RESULT_OUTPUTMAX)
throw MakeActivityException(this, 0, "Configured max result size, %d MB, exceeds absolute max limit of %d MB. A huge Dali result usually indicates the ECL needs altering.", workunitWriteLimit, DALI_RESULT_OUTPUTMAX);
assertex(workunitWriteLimit<=0x1000); // 32bit limit because MemoryBuffer/CMessageBuffers involved etc.
workunitWriteLimit *= 0x100000;
}
virtual void init()
{
CMasterActivity::init();
// In absense of OPT_OUTPUTLIMIT check pre 5.2 legacy name OPT_OUTPUTLIMIT_LEGACY
workunitWriteLimit = activityMaxSize ? activityMaxSize : getOptInt(OPT_OUTPUTLIMIT, getOptInt(OPT_OUTPUTLIMIT_LEGACY, defaultDaliResultLimit));
if (workunitWriteLimit>defaultDaliResultOutputMax)
throw MakeActivityException(this, 0, "Configured max result size, %d MB, exceeds absolute max limit of %d MB. A huge Dali result usually indicates the ECL needs altering.", workunitWriteLimit, defaultDaliResultOutputMax);
assertex(workunitWriteLimit<=0x1000); // 32bit limit because MemoryBuffer/CMessageBuffers involved etc.
workunitWriteLimit *= 0x100000;
}
CWorkUnitWriteActivityMaster(CMasterGraphElement * info) : CWorkUnitWriteGlobalMasterBase(info)
{
helper = (IHThorWorkUnitWriteArg *)queryHelper();
appendOutput = 0 != (POFextend & helper->getFlags());
flushThreshold = getOptInt(THOROPT_OUTPUT_FLUSH_THRESHOLD, -1);
resultName.set(helper->queryName());
resultSeq = helper->getSequence();
if (POFmaxsize & helper->getFlags())
activityMaxSize = helper->getMaxSize();
}
/**
* Compute genotypes
*/
void DmetEngine::computeGenotypes() {
ProbesetGenotypeEngine engine;
vector<string> celFiles = getOptVector("cels");
engine.setOpt("cels",celFiles);
vector<string> chipTypes = getOptVector("chip-type");
if(chipTypes.size() > 0)
engine.setOpt("chip-type",chipTypes);
engine.setOpt("cdf-file",getOpt("cdf-file"));
engine.setOpt("spf-file",getOpt("spf-file"));
string analysis;
if(getOpt("gt-analysis") != "") {
analysis = getOpt("gt-analysis");
} else {
///@todo If we have a reference, set analysis and qmethod-spec based on
/// what was used to build the reference
if(getOpt("reference-output") != "") {
analysis = "quant-norm.sketch=50000,pm-only,brlmm-p-multi.CM=1.bins=100.mix=1.bic=2.lambda=1.0.HARD=3.SB=0.75.KX=0.3.KH=0.3.KXX=0.1.KAH=-0.1.KHB=-0.1.KYAH=-0.05.KYHB=-0.05.KYAB=-0.1.transform=MVA.AAM=2.8.BBM=-2.8.AAV=0.10.BBV=0.10.ABV=0.10.V=1.AAY=10.7.ABY=11.3.BBY=10.7.copyqc=0.00000.wobble=0.05.MS=0.1.copytype=-1.clustertype=2.CSepPen=0.5.ocean=0.0000001";
} else {
analysis = "quant-norm.sketch=50000,pm-only,brlmm-p-multi.CM=2.bins=100.mix=1.bic=2.lambda=1.0.HARD=3.SB=0.75.KX=0.3.KH=0.3.KXX=0.1.KAH=-0.1.KHB=-0.1.KYAH=-0.05.KYHB=-0.05.KYAB=-0.1.transform=MVA.AAM=2.8.BBM=-2.8.AAV=0.10.BBV=0.10.ABV=0.10.V=1.AAY=10.7.ABY=11.3.BBY=10.7.copyqc=0.00000.wobble=0.05.MS=0.1.copytype=-1.clustertype=2.CSepPen=0.5.ocean=0.0000001";
}
analysis += ".cc-alleles=6";
analysis += ".cc-type=UCHAR";
analysis += ".cc-version=1.0";
}
if(getOpt("gt-qmethod-spec") != "")
engine.setOpt("qmethod-spec",getOpt("gt-qmethod-spec"));
else
engine.setOpt("qmethod-spec","plier.optmethod=1.FixFeatureEffect=true");
analysis = setPra(analysis,getOptInt("pra-thresh"));
engine.setOpt("analysis",analysis);
engine.setOpt("out-dir",Fs::join(getOpt("out-dir"),"apg"));
engine.setOpt("verbose",getOpt("verbose"));
engine.setOpt("force",getOpt("force"));
engine.setOpt("cc-chp-output","false");
engine.setOpt("probeset-ids-reported",getOpt("probeset-ids-reported"));
engine.setOpt("probeset-ids",getOpt("probeset-ids"));
engine.setOpt("temp-dir", getOpt("temp-dir"));
engine.setOpt("use-disk", getOpt("use-disk"));
engine.setOpt("disk-cache", getOpt("disk-cache"));
engine.setOpt("set-analysis-name", getOpt("set-analysis-name"));
engine.setOpt("call-coder-max-alleles", getOpt("call-coder-max-alleles"));
engine.setOpt("call-coder-type", getOpt("call-coder-type"));
engine.setOpt("call-coder-version", getOpt("call-coder-version"));
engine.setOpt("command-line", getOpt("command-line"));
engine.setOpt("exec-guid", getOpt("exec-guid"));
engine.setOpt("program-name", getOpt("program-name"));
engine.setOpt("program-company", getOpt("program-company"));
engine.setOpt("program-version", getOpt("program-version"));
engine.setOpt("program-cvs-id", getOpt("program-cvs-id"));
engine.setOpt("version-to-report", getOpt("version-to-report"));
engine.setOpt("prior-size", "1");
engine.setOpt("special-snps", getOpt("special-snps"));
engine.setOpt("em-gender", "false");
if(getOpt("chrX-probes") != "") {
engine.setOpt("chrX-probes", getOpt("chrX-probes"));
engine.setOpt("chrY-probes", getOpt("chrY-probes"));
engine.setOpt("set-gender-method", "cn-probe-chrXY-ratio");
engine.setOpt("no-gender-force", "false");
} else {
engine.setOpt("set-gender-method", "none");
engine.setOpt("no-gender-force", "true");
}
engine.setOpt("female-thresh", getOpt("female-thresh"));
engine.setOpt("male-thresh", getOpt("male-thresh"));
engine.setOpt("table-output", "false");
engine.setOpt("output-context", "true");
engine.setOpt("output-forced-calls", "true");
if (getOptBool("run-cn-engine") && getOpt("cn-region-gt-probeset-file") != "") {
/// @todo perhaps we should use state to track the file name
/// as it is we need to keep this in sync with the cn engine call
engine.setOpt("genotype-markers-cn-file",
Fs::join(getOpt("out-dir"),
"adc",
getOpt("set-analysis-name") + ".gt.markers.cn.call.a5"));
}
engine.setOpt("a5-global-file",getOpt("reference-output"));
engine.setOpt("a5-global-file-no-replace","true");
engine.setOpt("a5-group","ProbesetGenotypeEngine");
engine.setOpt("a5-calls","true");
engine.setOpt("a5-summaries","true");
engine.setOpt("a5-feature-effects","true");
engine.setOpt("a5-sketch","true");
engine.setOpt("a5-write-models","true");
if(getOpt("reference-output") != "") {
engine.setOpt("a5-sketch-use-global","true");
engine.setOpt("a5-feature-effects-use-global","true");
engine.setOpt("a5-write-models-use-global","true");
}
engine.setOpt("a5-global-input-file",getOpt("reference-input"));
engine.setOpt("a5-input-group","ProbesetGenotypeEngine");
if(getOpt("reference-input") != "") {
engine.setOpt("a5-sketch-input-global","true");
engine.setOpt("a5-feature-effects-input-global","true");
engine.setOpt("a5-models-input-global","true");
}
if(m_ArgvPosAPG > 0)
engine.parseArgv(m_argv, m_ArgvPosAPG);
engine.run();
}
