Method run

src/rnabloom/RNABloom.java:3699–3859

()

        }
        
        @Override
        public void run() {
            //boolean stranded = graph.isStranded();
            
            try {                
                String[] nameSeqPair;
                while((nameSeqPair = itr.next()) != null) {
                    ++numReads;
                    String seq = reverseComplement ? reverseComplement(nameSeqPair[1]) : nameSeqPair[1];
                    boolean kept = false;
                                      
                    if (seq.length() >= k) {
                        String name = nameSeqPair[0];
                                                
                        boolean hasPolyA = false;
                        
                        if (minPolyATailLengthRequired > 0) {                            
                            Interval tailRegion = polyaFinder.findPolyATail(seq);
                            if (strandSpecific) {
                                if (tailRegion != null && tailRegion.end < seq.length()) {
                                    seq = seq.substring(0, tailRegion.end);
                                    hasPolyA = true;
                                }
                            }
                            else {
                                Interval headRegion = polyaFinder.findPolyTHead(seq);

                                if (tailRegion != null && headRegion == null) {
                                    if (tailRegion.end < seq.length()) {
                                        seq = seq.substring(0, tailRegion.end);
                                    }
                                    hasPolyA = true;
                                }
                                else if (tailRegion == null && headRegion != null) {
                                    if (headRegion.start > 0) {
                                        seq = seq.substring(headRegion.start);
                                    }
                                    seq = reverseComplement(seq);
                                    hasPolyA = true;
                                }
                                else if (tailRegion != null && headRegion != null) {                                    
//                                    boolean hasPas = polyaFinder.hasPolyASignal(seq, tailRegion.start);
//                                    boolean hasPasRC = polyaFinder.hasPolyASignalRC(seq, headRegion.end);
//                                    
//                                    if (hasPas && !hasPasRC) {
//                                        if (headRegion.end < tailRegion.end) {
//                                            // remove polyT head
//                                            seq = seq.substring(headRegion.end, tailRegion.end);
//                                            hasPolyA = true;
//                                        }
//                                    }
//                                    else if (!hasPas && hasPasRC) {
//                                        if (headRegion.start < tailRegion.start) {
//                                            // remove polyA tail
//                                            seq = reverseComplement(seq.substring(headRegion.start, tailRegion.start));
//                                            hasPolyA = true;
//                                        }
//                                    }