>I’ve finally “finished” the manual for one section of the Vancouver Short Read Analysis Package – though it’s not findpeaks. (I’m still working on that – but it’s a big application.) It could still use pictures and graphs, and stuff… but it’s now functional.
One down… about 7 more manuals to write. Documentation is never the fun stuff.
What slowed this down, ironically, was my inabilty to read the Maq documentation. I completely missed the fact that unmapped reads are now included in PET aligned .map files, but with a different paired flag status. Previously, unmapped ends were thrown away, and I had to handle the unpaired ends. With the new version, those unmapped reads are now included, but given a status of 192, so they can be paired again – albeit there’s not much information in the pairing. Infact, I can even handle the other ends as I find them, because they’re given a status of 64. (Do these numbers seem arbitrary to anyone other than me?)
Anyhow, Finally, the .map to .bed converter works – and there’s a manual to go with it.