// constructor
public TQuery(String[] args) {
try {
long startTime = System.currentTimeMillis();
processArgs(args);
queryIndex = new QueryIndex(this);
queryLoader = new QueryLoader(this);
// print some stats on building the engine
String diffTime =
Num.formatNumberOneFraction(((double) (System.currentTimeMillis() - startTime)) / 1000);
int numFiles = vcfDataFiles.length + bedDataFiles.length + mafDataFiles.length;
System.err.println("\n" + diffTime + " Sec to build using " + IO.memory() + " of RAM");
System.err.println("\t" + numFiles + "\tData sources loaded");
System.err.println("\t" + dataSources.getRecordsLoaded() + "\tRecords indexed");
System.err.println("\t" + dataSources.getRecordsSkipped() + "\tRecords skipped\n");
// print summary of available filters
System.err.println(dataSources.fetchSummary());
queryFilesFromCmdLine();
// release file handles
queryLoader.closeTabixReaders();
} catch (Exception e) {
e.printStackTrace();
System.err.println("\nProblem with executing the TQuery!");
}
}
/**
* Makes a stair step heat map from an array of windows in bar format. One per chromosome. Don't
* forget to set the barDirectory and score Index!!!!!!!
*/
public void makeStairStepBarFiles() {
// make bar parser
BarParser bp = new BarParser();
bp.setZipCompress(true);
HashMap<String, String> tagVals = new HashMap<String, String>();
tagVals.put(BarParser.GRAPH_TYPE_TAG, BarParser.GRAPH_TYPE_STAIRSTEP);
tagVals.put(BarParser.GRAPH_TYPE_COLOR_TAG, "#FF00FF"); // fusha
tagVals.put(BarParser.SOURCE_TAG, bedFile.toString());
// for each chromosome
System.out.print("Printing... ");
Iterator<String> it = bedLinesHash.keySet().iterator();
while (it.hasNext()) {
chromosome = it.next();
System.out.print(chromosome + " ");
windows = bedLinesHash.get(chromosome);
// add blocks
assembleBlocks();
// balance by adding max or min at zero base
balanceValues();
// write bar file
File barFile = new File(barDirectory, chromosome + ".bar");
bp.writeBarFile(
barFile,
chromosome,
genomeVersion,
'.',
Num.arrayListOfIntegerToInts(bases),
Num.arrayListOfFloatToArray(values),
tagVals);
// clear ArrayLists
bases.clear();
values.clear();
}
System.out.println();
}
/**
* Chr\tPos\tRef\tAlt\tName\tSampleNames\tRefAltCounts\tTotalRef\tTotalAlt\tSampleGCScores\tFDR\tLog2Rto\tBadHetCall?
*/
public String toString(boolean skipGeneral) {
StringBuilder sb = new StringBuilder();
if (skipGeneral == false) {
sb.append(chromosome);
sb.append("\t");
sb.append(position);
sb.append("\t");
sb.append(reference);
sb.append("\t");
sb.append(alternate);
sb.append("\t");
sb.append(name);
sb.append("\t");
}
int numRef = 0;
int numAlt = 0;
if (sampleName != null) {
// sampleNames
String sampleNames = Misc.stringArrayListToString(sampleName, ",");
sb.append(sampleNames);
sb.append("\t");
// ref/alt counts
int[] refAltCounts = getRefAltCounts(gatcnCounts.get(0));
sb.append(refAltCounts[0]);
sb.append("_");
sb.append(refAltCounts[1]);
numRef += refAltCounts[0];
numAlt += refAltCounts[1];
for (int i = 1; i < gatcnCounts.size(); i++) {
sb.append(",");
refAltCounts = getRefAltCounts(gatcnCounts.get(i));
sb.append(refAltCounts[0]);
sb.append("_");
sb.append(refAltCounts[1]);
numRef += refAltCounts[0];
numAlt += refAltCounts[1];
}
sb.append("\t");
// totals
sb.append(numRef);
sb.append("\t");
sb.append(numAlt);
sb.append("\t");
// sample scores
float[] s = Num.arrayListOfFloatToArray(sampleGCScore);
String scores = Misc.floatArrayToString(s, ",");
sb.append(scores);
sb.append("\t");
// fdr
sb.append(fdr);
sb.append("\t");
// log2Rto
sb.append(log2Ratio);
// bad het call?
if ((numRef + numAlt != 0) && (numRef == 0 || numAlt == 0)) sb.append("\ttrue");
else sb.append("\tfalse");
// gene names?
if (geneNames != null) {
sb.append("\t");
sb.append(Misc.stringArrayListToString(geneNames, ","));
}
}
return sb.toString();
}
public boolean passMinCoverage(int minimumReadCoverage) {
for (int i = 0; i < gatcnCounts.size(); i++) {
if (Num.sumIntArray(gatcnCounts.get(i)) >= minimumReadCoverage) return true;
}
return false;
}