Hi Ozgur,
I personally found the paper describing HPC to be quite descriptive.
See especially section 3.3 - it seems like it would be possible to
hack something up to remove entries containing "error" for example.
That being said, I can't find any reference to the program
"hpc-makemtix" aside from that paper. Maybe it got folded back into
hpc? Did you make any progress with this?
http://www.cs.york.ac.uk/plasma/publications/pdf/GillRuncimanHW07.pdf