private void reportErrorParsingLine(String reason, final SAMValidationError.Type type, final Throwable nestedException) { reason = "Error parsing SAM header. " + reason + ". Line:\n" + mCurrentLine; if (validationStringency != ValidationStringency.STRICT) { final SAMValidationError error = new SAMValidationError(type, reason, null, mReader.getLineNumber()); error.setSource(mSource); mFileHeader.addValidationError(error); } else { String fileMessage = ""; if (mSource != null) { fileMessage = "File " + mSource; } throw new SAMFormatException(reason + "; " + fileMessage + "; Line number " + mReader.getLineNumber(), nestedException); } }
private void reportErrorParsingLine(String reason, final SAMValidationError.Type type, final Throwable nestedException) { reason = "Error parsing SAM header. " + reason + ". Line:\n" + mCurrentLine; if (validationStringency != ValidationStringency.STRICT) { final SAMValidationError error = new SAMValidationError(type, reason, null, mReader.getLineNumber()); error.setSource(mSource); mFileHeader.addValidationError(error); } else { String fileMessage = ""; if (mSource != null) { fileMessage = "File " + mSource; } throw new SAMFormatException(reason + "; " + fileMessage + "; Line number " + mReader.getLineNumber(), nestedException); } }
private void reportErrorParsingLine(String reason, final SAMValidationError.Type type, final Throwable nestedException) { reason = "Error parsing SAM header. " + reason + ". Line:\n" + mCurrentLine; if (validationStringency != ValidationStringency.STRICT) { final SAMValidationError error = new SAMValidationError(type, reason, null, mReader.getLineNumber()); error.setSource(mSource); mFileHeader.addValidationError(error); } else { String fileMessage = ""; if (mSource != null) { fileMessage = "File " + mSource; } throw new SAMFormatException(reason + "; " + fileMessage + "; Line number " + mReader.getLineNumber(), nestedException); } }