Hello, the 10th coding week began and we are getting closer to our goal. The current version of the transalign program is faster than the original version and needs less memory (34 GB) than the original one (53 GB). Last week I worked on this and replaced an IntMap by a HashMap in the program. Here is the blog post: http://biohaskell.org/GSoC_blog/Weeks_8and9
This week I will try to reduce the memory consumption a bit more such that it will be possible to run the program on a standard computer. For this purpose, I will try to include Judy arrays. Here is the blog post for the 10th week: http://biohaskell.org/GSoC_blog/Weeks_10and11 Have a nice week, Sarah
