Method write

src/rnabloom/RNABloom.java:1639–1779

(String fragment, ArrayList<Kmer> transcriptKmers)

        }
                
        public synchronized void write(String fragment, ArrayList<Kmer> transcriptKmers) throws IOException {            
            if (!represented(transcriptKmers,
                                graph,
                                screeningBf,
                                lookahead,
                                maxIndelSize,
                                maxTipLength,
                                percentIdentity)) {

                String transcript = graph.assemble(transcriptKmers);
                ArrayDeque<Integer> pasPositions = null;
                
                boolean txptReverseComplemented = false;
                if (minPolyATailLengthRequired > 0) {
                    boolean hasPolyATail = polyATailOnlyPattern.matcher(transcript).matches();
                    boolean hasPolyTHead = false;
                    
                    if (strandSpecific) {
                        pasPositions = getPolyASignalPositions(transcript, polyASignalPattern, polyATailOnlyMatchingPattern);
                    }
                    else {
                        hasPolyTHead = polyTHeadOnlyPattern.matcher(transcript).matches();
                        
                        if (hasPolyATail) {
                            pasPositions = getPolyASignalPositions(transcript, polyASignalPattern, polyATailOnlyMatchingPattern);
                        }
                        
                        if (hasPolyTHead && (pasPositions == null || pasPositions.isEmpty())) {
                            String transcriptRC = reverseComplement(transcript);
                            
                            pasPositions = getPolyASignalPositions(transcriptRC, polyASignalPattern, polyATailOnlyMatchingPattern);
                            
                            if (!pasPositions.isEmpty()) {
                                transcript = transcriptRC;
                                txptReverseComplemented = true;
                            }
                        }
                    }
                }
                                
                for (Kmer kmer : transcriptKmers) {
                    screeningBf.add(kmer.getHash());
                }
                
                int len = transcript.length();
                float cov = getMedianKmerCoverage(transcriptKmers);
                
                StringBuilder headerBuilder = new StringBuilder();
                headerBuilder.append(prefix);
                headerBuilder.append(++cid);
                headerBuilder.append(" l=");
                headerBuilder.append(len);
                headerBuilder.append(" c=");
                headerBuilder.append(String.format("%.1f", cov));
                if (!fragment.isEmpty()) {
                    headerBuilder.append(" F=[");
                    headerBuilder.append(fragment);
                    headerBuilder.append("]");