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inamnh/PCG (press backspace or delete to remove)Previously we were statically linking but doing that with glibc is a big problem (see here). It is recommended instead
to use musl for static linking.
Boarders
- 1
- Opened on Nov 30, 2021
- #167
We currently generate invalid implied alignment. The pre-order traversal of implied alignment algorithm relies on
knowing if the current node is the left or right child of it s parent. This information ...
defect
recursion-ninja
- 1
- Opened on Jun 28, 2020
- #166
Currently on master several of the tests to do with dynamic character decoding fail (with some throwing exceptions). I
eventually tracked down that this is an error in the unsorted branch of the getSubsetIndex ...
defect
- 3
- Opened on Jun 3, 2020
- #165
The problem
Currently our character data is represented as follows:
newtype ContinuousCharacter = CC (ExtendedReal, ExtendedReal)
-- where for the sake of completeness ExtendedReal is defined as:
newtype ...
enhancement
performance/optimization
refactor
- 5
- Opened on Mar 25, 2020
- #164
Ward mentioned that we should add a new build method which uses the distance Wagner. This is described in detail on
p. 165 of the Systematics text book. Roughly it works as follows: given an already constructed ...
enhancement
performance/optimization
- 5
- Opened on Feb 27, 2020
- #163
Currently our project can be very painful to build on a fresh machine if it is not easy to grab the correct versions of
GHC and cabal. Nix is a package manager for both mac and linux that should, in theory, ...
enhancement
- 8
- Opened on Feb 27, 2020
- #162
The user guide gives various options for runtime parameters particularly for tuning the garbage collector. We should
experiment with changing the allocation area of the program to see if this makes a difference ...
performance/optimization
- 4
- Opened on Jan 17, 2020
- #161
The alpha version of ghc-8.10.x is out.
We should test our project s compatibility as early as possible.
We can (currently) build our project with the new compiler on the ghc-8.10 branch.
The only trouble ...
low priority
- 2
- Opened on Nov 28, 2019
- #160
When running pcg-test-flu-net with the following script:
read( flu_small_hxnx_hsa_seg1_PB2.fasta )
read( flu_small_hxnx_hsa_seg2_PB1.fasta )
read( flu_small_hxnx_hsa_seg3_PA.fasta )
read( flu_small_hxnx_hsa_seg4_HA.fasta ...
defect
- Opened on Nov 19, 2019
- #159
We repeat ourselves a lot in our various sub libraries. One such example is the GHC flags which are the same in every
library.
cabal promises to reduce duplication with multiple public libraries and common ...
low priority
refactor
- 1
- Opened on Nov 15, 2019
- #158
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