double terminator trouble

[kristofer]

So I compiled the code, and tried to run a small text file thru the encode script...

'''
kristofer@black:~/DNAcodec/DNAcodec$ scripts/run_encode.sh machiavelli.txt machiavelli.bin
Encoded 3 blocks, source block size 512, encoded block size 1024
Position 472 to 512 of the last block was padded with double terminator
-:48: parser error : Extra content at the end of the document
?????????????????????????????????????????????????????????????????????????
^
scripts/run_encode.sh: line 8: 17212 Done lzma -z -9 -c $1
17213 Broken pipe | ./encode ECC.pchk ECC.gen - -
17214 Segmentation fault | ./DNAIO -f - $2
'''

If I break out the three steps of the script, skipping the lempel-ziv compress, just run ./encode ...
I end up with an intermediate file that has about a gigabyte of \377's after the last xml element.

I am running on this on a ubuntu box of recent release...

any ideas? Maybe you're not closing the tmp file before you copy to the output (or something?)

[a113n]

Thanks for reporting this bug! I will look into this issue.

[a113n]

Hi Kristofer,

I can't reproduce this bug, can you send me a minimal excerpt of your file that can cause such bug?

Thanks!
Allen