Inconsistency in Read and Write of Body of an Attachment

I am trying to create an Attachment as follows:
SObject creatable= new SObject();
creatable.setType(objectType);
creatable.setField("Name", "sfdcTest1.pdf");
creatable.setField("ParentId", "a0I2300000BbZ1S");

InputStream in = new FileInputStream("C:\dev\java\workspace\sforce-soap-jar\src\sfdcTest1.pdf");
String body = base64Encode(in);// Step-A. this method base64 encodes the content of the input stream
byte[] bodyBytes = body.getBytes(Charsets.UTF_8);
in.close();
creatable.setField("Body", bodyBytes);
connection.create(new SObject[]{creatable});

This returns a successful response but when I try to open this attachment in Chrome browser after logging into my salesforce organization, it says "'Failed to load PDF document".
On investigating further, I found that if I do not base64 encode at Step-A, then everything works fine. Looks like the jar performs the base64 encoding by itself.
But then, if I try to retrieve the same Attachment's body back, then I am having to do base64 decoding on my own. So, both operations, read and write are not consistent. The jar should either do both encoding as well as decoding on it's own or not do anything at all. However, right now, it's encoding while creating but not decoding while retrieving.