thanks everyone for the reply
we have got a workaround for this problem. instead of keeping the data in sequential and then calling the java file to access the file, we placed the data in a dataset and the called the java class from the java tranformer stage which will write the data into another dataset.
New line character issue for sequential file stage
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New line character issue for sequential file stage
iam assuming you have a transformer in the job. in our case we dont have a transformer stage and we are not sure in which column does the new line character comes. and also we dont want to use the convert() funtion for all the columns in the transformer. that is the reason why we went with java transformer stage.