Commits

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Author Commit Message Labels Comments Date
Mark Howison
debruijn: added extra round of merging redundant nodes
Branches
2 branches
Mark Howison
graph: fixed bug where both endpoints weren't always in starting pathset
Branches
2 branches
Mark Howison
sampler: added additional debug info on Bowtie2/LAP error
Branches
2 branches
Mark Howison
sample: added debug output at each perturbatino in the current timestep
Branches
2 branches
Mark Howison
report: switched to SVG images
Branches
4 branches
Mark Howison
graph: random walk now stops if it intersects itself
Branches
4 branches
Mark Howison
calc_prob: fixed error message in SAM pars=ing exception
Branches
4 branches
Mark Howison
Merge branch 'devel' of bitbucket.org:mhowison/gabi into devel
Branches
5 branches
Mark Howison
Merge branch 'master' into devel
Branches
5 branches
Mark Howison
hotfix: phix-test/00-subset-data.sh: filter_illumina name change
Mark Howison
pulled LAP into GABI and replaced SeqIO module with Bio.SeqIO
Branches
5 branches
Mark Howison
new option to sample to load an existing assembly as the initial state
Branches
5 branches
Mark Howison
Merge branch 'master' into devel
Branches
5 branches
Mark Howison
0.2.0
Mark Howison
updated phix report
Branches
5 branches
Mark Howison
bumped version to 0.2.0 and added autogen.sh
Branches
5 branches
Mark Howison
NEWS for 0.2.0
Branches
5 branches
Mark Howison
updated description of phix-test
Branches
5 branches
Mark Howison
README: updated BioLite prereq to 0.4.0
Branches
5 branches
Mark Howison
fixed majority rule FASTA output
Branches
5 branches
Mark Howison
report: added table of node frequencies
Branches
5 branches
Mark Howison
report: fixed bug in colormap for coloring by frequency
Branches
5 branches
Mark Howison
updated phix-test scripts
Branches
5 branches
Mark Howison
report: use bold stroke to indicate current assembly in trace animation
Branches
5 branches
Mark Howison
graph: fixed bug in deactivating path in perturb_path()
Branches
5 branches
Mark Howison
debugged and restyled report
Branches
5 branches
Mark Howison
updates to report and plots to support new db schema
Branches
5 branches
Mark Howison
sampler: fixed conversion of scale to float
Branches
5 branches
Mark Howison
store edges/nodes as list directly in samples table
Branches
5 branches
Mark Howison
sampler is more robust to nan and -inf
Branches
5 branches
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