()
| 758 | } |
| 759 | |
| 760 | @Override |
| 761 | public void run() { |
| 762 | System.out.println("[" + id + "] Parsing `" + path + "`..."); |
| 763 | |
| 764 | try { |
| 765 | Matcher mSeq = seqPattern.matcher(""); |
| 766 | long[] hashVals = itr.hVals; |
| 767 | |
| 768 | if (FastqReader.isCorrectFormat(path)) { |
| 769 | FastqReader fr = minAvgBaseQual > 0 ? new FastqFilteredReader(path, minAvgBaseQual) : new FastqReader(path); |
| 770 | Matcher mQual = qualPattern.matcher(""); |
| 771 | |
| 772 | FastqRecord record = new FastqRecord(); |
| 773 | |
| 774 | if (storeReadPairedKmers) { |
| 775 | long[] phashVals = pitr.hValsP; |
| 776 | |
| 777 | while (fr.hasNext()) { |
| 778 | fr.nextWithoutName(record); |
| 779 | |
| 780 | if (record.seq.length() < k) { |
| 781 | // skip to next read |
| 782 | continue; |
| 783 | } |
| 784 | |
| 785 | mQual.reset(record.qual); |
| 786 | mSeq.reset(record.seq); |
| 787 | |
| 788 | while (mQual.find()) { |
| 789 | mSeq.region(mQual.start(), mQual.end()); |
| 790 | while (mSeq.find()) { |
| 791 | int start = mSeq.start(); |
| 792 | int end = mSeq.end(); |
| 793 | |
| 794 | if (itr.start(record.seq, start, end)) { |
| 795 | while (itr.hasNext()) { |
| 796 | itr.next(); |
| 797 | addFunction.accept(hashVals); |
| 798 | } |
| 799 | |
| 800 | if (pitr.start(record.seq, start, end)) { |
| 801 | while (pitr.hasNext()) { |
| 802 | pitr.next(); |
| 803 | graph.addReadSingleKmerPair(phashVals); |
| 804 | } |
| 805 | } |
| 806 | } |
| 807 | } |
| 808 | } |
| 809 | |
| 810 | ++numReads; |
| 811 | } |
| 812 | } |
| 813 | else { |
| 814 | while (fr.hasNext()) { |
| 815 | fr.nextWithoutName(record); |
| 816 | |
| 817 | if (record.seq.length() < k) { |
nothing calls this directly
no test coverage detected