Method getLengthNormalizedReadCounts

src/rnabloom/olc/Layout.java:4480–4505

(String pafPath, Set<String> skipSet)

    }
    
    public HashMap<String, Float> getLengthNormalizedReadCounts(String pafPath, Set<String> skipSet) throws IOException {
        HashMap<String, Float> counts = new HashMap<>();
                
        PafReader reader = new PafReader(pafPath);
        String prevName = null;
        ArrayList<StrandedOverlap> targets = new ArrayList<>();
        for (PafRecord r = new PafRecord(); reader.hasNext();) {
            reader.next(r);
            
            if (!r.qName.equals(prevName)) {
                updateCounts(targets, counts);
                targets = new ArrayList<>();
                prevName = r.qName;
            }
            
            if (!skipSet.contains(r.tName)) {
                targets.add(pafToStrandedOverlap(r));
            }
        }
        reader.close();
        
        // process the last batch of records
        updateCounts(targets, counts);
        
        return counts;
    }
    
    public static void main(String[] args) {
        try {