private FastqRecord readNextRecord() { try { final String seqHeader = readLineConditionallySkippingBlanks(); if (seqHeader == null) return null ; if (StringUtil.isBlank(seqHeader)) { final String seqLine = readLineConditionallySkippingBlanks(); checkLine(seqLine, LineType.SequenceLine); final String qualHeader = readLineConditionallySkippingBlanks(); checkLine(qualHeader, LineType.QualityHeader); if (!qualHeader.startsWith(FastqConstants.QUALITY_HEADER)) { final String qualLine = readLineConditionallySkippingBlanks(); checkLine(qualLine, LineType.QualityLine);
private FastqRecord readNextRecord() { try { final String seqHeader = readLineConditionallySkippingBlanks(); if (seqHeader == null) return null ; if (StringUtil.isBlank(seqHeader)) { final String seqLine = readLineConditionallySkippingBlanks(); checkLine(seqLine, LineType.SequenceLine); final String qualHeader = readLineConditionallySkippingBlanks(); checkLine(qualHeader, LineType.QualityHeader); if (!qualHeader.startsWith(FastqConstants.QUALITY_HEADER)) { final String qualLine = readLineConditionallySkippingBlanks(); checkLine(qualLine, LineType.QualityLine);
final String seqHeader = readLineConditionallySkippingBlanks(); if (seqHeader == null) return null ; if (StringUtil.isBlank(seqHeader)) { final String seqLine = readLineConditionallySkippingBlanks(); checkLine(seqLine,"sequence line"); final String qualHeader = readLineConditionallySkippingBlanks(); checkLine(qualHeader,"quality header"); if (!qualHeader.startsWith(FastqConstants.QUALITY_HEADER)) { final String qualLine = readLineConditionallySkippingBlanks(); checkLine(qualLine,"quality line");