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hyanwong
/
giglib
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4
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1
Issues:
68
Forks:
2
hyanwong/giglib Issues
Change repo name to "giglib"
Closed
4 months ago
Choose breakpoints by rejection sampling
Updated
4 months ago
Comments count
1
"Pseudo-Roots" and representing ancestral variation
Updated
4 months ago
Implement a basic simplify()
Updated
4 months ago
Comments count
2
Inference from real data: useful references
Updated
4 months ago
Comments count
2
Speed up forward simulations
Updated
4 months ago
Comments count
4
Allow easy editing of table data
Closed
7 months ago
Comments count
1
Make the mrca structure into a class
Closed
7 months ago
Comments count
6
Account for chromosome IDs when tracing intervals
Closed
7 months ago
Comments count
4
Adjust MRCA routines to account for different chromosomes
Closed
7 months ago
Comments count
1
Change to sorting by child_right (not child_left)?
Closed
7 months ago
Comments count
2
Transposable element (TE) simulations
Updated
7 months ago
More efficient seq_len calculation
Closed
8 months ago
Comments count
1
Storing length of the genome
Closed
8 months ago
Comments count
3
Use numpy structured array for iedge table
Closed
8 months ago
Comments count
2
IntFlags in constants.py changes behaviour under python 3.11 (vs 3.10)
Closed
8 months ago
Comments count
1
Documentation via JupyterBook (and tidy)
Updated
8 months ago
Comments count
5
Extracting haplotypes / DNA sequences
Updated
8 months ago
Finding "next most close" MRCAs
Updated
8 months ago
Requirements for a valid GIG (and for a valid `gigl` encoding)
Closed
8 months ago
Comments count
5
Construct more GIG examples with combinations of SVs and recombination
Updated
8 months ago
Comments count
12
Should GIGs be allowed to have a node at time=infinity?
Closed
8 months ago
Comments count
2
Test fwd-sim code with duplications
Updated
8 months ago
Backward simulations: a possible breakthrough?
Updated
8 months ago
Comments count
1
Think about edge ordering for backward-time simulations
Updated
8 months ago
Encoding inversions, and integer positions
Closed
10 months ago
Comments count
14
Validate edges on add_row
Closed
8 months ago
Comments count
6
Test fwd-sim with a single inversion
Closed
8 months ago
Comments count
1
Efficient interval intersections
Updated
8 months ago
Comments count
3
Graph traversal algorithm for matching
Closed
9 months ago
Comments count
5
Test empty GIGs
Closed
9 months ago
Comments count
1
Move table validation into tables.py
Updated
9 months ago
Storing (L, R) plus value for inverted
Updated
9 months ago
Comments count
2
Introducing SVs into the forward simulator
Closed
9 months ago
Comments count
2
How to *stop* weird crossovers
Updated
9 months ago
Ideas for visualisation tools
Updated
9 months ago
Comments count
1
Order edges by child time (and ID)?
Closed
9 months ago
Comments count
2
Check that coordinates can be converted to integers in `append` and `add_row`
Closed
10 months ago
Comments count
1
Order of iedge items
Closed
10 months ago
Comments count
4
Long-term API ideas: named accessors
Updated
10 months ago
Restricted simulation that can be simulated backwards and forwards
Updated
10 months ago
Comments count
2
Changes to tskit-like API
Closed
10 months ago
Comments count
2
Define a "TreeSequence"-like class
Closed
10 months ago
Comments count
10
When to check GIG consistency
Closed
a year ago
Comments count
3
Switch to integer coordinate space
Closed
a year ago
Comments count
2
Rename "Interval" or "Edge" to "IEdge"
Closed
a year ago
Comments count
2
Get tsdate-like algorithms running on a GIG
Updated
a year ago
Explore simulations without recombination for cancer genomes
Updated
a year ago
Make method to convert a GIG table into a Pandas dataframe
Closed
a year ago
Comments count
4
Algorithm to find the tree for a point on the genome of a given sample
Updated
a year ago
Comments count
5
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