In some cases repeated mappings against the same reference will result in a dramatically reduced runtime because the internal data structure used for mapping the reads, which is reference specific, can be reused. This has been enabled by storing files in the system tmp folder as a caching mechanism. Only a certain amount of disk space will be used and once reaching the limit, the oldest files are cleaned up. Consequently, the reference data structure files will automatically have to be recreated if the cache was filled or the tmp folder was cleaned up.
The default space limit is 8 GB which can be changed by going to
Edit | Preferences | Advanced | Read Mapper
On the server and for webstart the cache size can be controlled by creating a settings file "readmapper.properties" with an entry going like this "referencecachesize = 8589934592" where the size is in bytes. On grid setups, the "readmapper.properties" file will have to be added manually to each grid worker directory.