Package org.bioinfo.ngs.qc.qualimap.beans

Examples of org.bioinfo.ngs.qc.qualimap.beans.SingleReadData


    static private SingleReadData getWindowData(Long windowStart, HashMap<Long,SingleReadData> resultsMap) {
        if (resultsMap.containsKey(windowStart)) {
            return resultsMap.get(windowStart);
        } else {
            SingleReadData data = new SingleReadData(windowStart);
            resultsMap.put(windowStart, data);
            return data;
        }
    }
View Full Code Here


                                         int mappingQuality) {

        long windowSize = window.getWindowSize();
        long windowStart = window.getStart();

        SingleReadData readData = getWindowData(windowStart, analysisResults);

        // working variables
        boolean outOfBounds = false;
        long relative;
        int pos;

        if(readEnd < readStart){
            System.err.println("WARNING: read alignment start is greater than end: " + readStart + " > " + readEnd);
        }

        //readData.numberOfProcessedReads++;
        if(readEnd> window.getEnd()){
            outOfBounds = true;
            //readData.numberOfOutOfBoundsReads++;
        }


        // run read
        for(long j=readStart; j<=readEnd; j++){
            relative = (int)(j - windowStart);
            pos = (int)(j-readStart);

            if(relative<0){

            } else if(relative >= windowSize){
                //  System.err.println("WARNING: " + read.getReadName() + " is fuera del tiesto " + relative);
                break;
            } else {

                if (analyzeRegions) {
                    boolean insideOfRegion = window.getSelectedRegions().get((int)relative);
                    if (insideOfRegion) {
                        if (computeOutsideStats) {
                            readData =getWindowData(windowStart, analysisResults);
                            //statsCollector = insideCollector;
                        }
                    } else {
                        if (computeOutsideStats) {
                            readData = getWindowData(windowStart, outOfRegionsResults);
                            //statsCollector = outsideCollector;
                        } else {
                            continue;
                        }
                    }
                }

                char nucleotide = alignment[pos];

                // aligned bases
                readData.numberOfMappedBases++;

                if (nucleotide != '-' && nucleotide != 'N') {
                    // mapping quality
                    readData.acumMappingQuality(relative, mappingQuality);
                    // base stats
                    readData.acumBase(relative, nucleotide);
                }

            }

View Full Code Here

TOP

Related Classes of org.bioinfo.ngs.qc.qualimap.beans.SingleReadData

Copyright © 2018 www.massapicom. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.