Small issue with halWriteNucleotides (?fix described)

[lukebharrison]

Hi,

I was working with the ancestorsML + halWriteNucleotides workflow and was having halWriteNucleotides crash with the following error:
command: halWriteNucleotides test.hal Anc01only.txt

terminate called after throwing an instance of 'hal_exception'
what(): DnaAccess is dirty, flush() should have been called
Aborted (core dumped)

Where Anc01only.txt is the output from ancestorsML with the --printWrites option

I added the following line to halWriteNucleotides.cpp:
after line 60: dnaIt->setBase(newChar);
dnaIt->flush();

This seems to have fixed the problem and halWriteNucleotides seems to be correctly updating the sequence in my HAL file. I am not an expert on the hal package, so I hope this is the correct fix - if not, please advise!

Thanks,

Luke.