| 12/24/2005 |
1.0 → 2.0 |
- Additions:
- Provision to specify target SNPs to be tagged.
- Allowed to specify multiple target SNP ranges using a range file.
- Allowed for a user defined property for each SNP (using the map file). This property can be used
to choose among solutions. By default, this option also outputs the two tagSNP sets obtained by maximizing and minimizing this
property among all the tagSNP sets. The --nsols option has to be specified to obtain these sets.
- Added a --c5 option, which gives all 5 criteria solutions. This, in effect replaces the -c option of old. Now, the -c option
only gives 3 criteria solutions.
- Added a default tagSNP set to the output files. This is one of the many tagSNP sets found by FESTA. Please note that this
set does not possess any special property.
- Modifications:
- Changed the way greedy-exhaustive algorithm works. Reversed the order of greedy and exhaustive searches. Now, an exhaustive
search is performed first and a greedy alogrithm is applied to the residual graphs. The limit on the number of exhaustive searches
is less than the computational limit that is use-specifiable. This limit is currently set to 10,000 solutions.
- Changed the -c option. It used to give 5 tag set solutions. It now gives only 3 solutions, which correspond to the first three
solutions earlier.
- Changed the output naming scheme. The -o option now acts as a prefix for the output files. The various output files are
preceded by this prefix string.
- Deletions:
- Removed the -N option to count number of double coverage solutions.
- Removed the -D option for coverage on a dense map using seed from a sparse map.
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