MAQ 0.7.1 binary map files

I took a look at the Maq 0.7.1 today, with the intent of getting the new .map files into the Vancouver Short Read Analysis package (Both FindPeaks and SNP calling). It turned out to be a very quick job. The only difference between version 0.6 and 0.7.1 is that the seq length constant in the core of the .map file can now be 128 or 64, whereas the older version only allowed 64.

Unfortunately, the Maq authors didn't include a flag in the header to specify which constant was used when a given .map file was created. In fact, there is no way to tell (as far as I know) from the binary file except to try opening it with one or the other - and see if you get garbage reads.

Anyhow, I figured I'd share that, in case anyone else is looking to use Maq 0.7.1.

Otherwise, the only other map file related difference between the versions (it was pointed out to me, but I had the opportunity to observe for myself as well), is that Maq 0.7.1 no longer writes out the .map files as the reads are processed - it's now all held in memory till the complete set of alignments is complete, and then is all dumped to disk at once. I'm not sure why that is, but it's an interesting difference, none the less.