Peppy, up until now, only digested chromosomes inside of open reading frames. This is no more. There is now choice! In the properties file you can set if you want to digest the whole chromosome or only the ORFs. Read More

in Spectrum.m. It’s a minor retooling of readPKL. Working on combining the two…. Read More

In matchTagsFiltered I noticed this comment “if the tag did not match then check for the Bion tag”. Thing is, there was no if clause governing this. It was going ahead and checking for the B ion all the time. I don’t know if this is desired or not, but I added code to make [...] Read More

Regarding Wednesday’s post, I am finding it difficult to believe that an int array is outperforming a char array in some cases. Especially when the code for the int array requires a few extra lines. Am beginning today with a quick sanity check–am cleaning the target with the char array code and running the test [...] Read More