Commits

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Author Commit Message Labels Comments Date
Mark Howison
sampler: use empirical prior distribution of lengths/ncontigs
Branches
issue-7
Mark Howison
fixed errors with report
Branches
issue-7
Mark Howison
sample: added dot output for candidate assembly
Branches
issue-7
Mark Howison
sampler: fixed calls to RSEM (1.2.15)
Branches
issue-7
Mark Howison
updated sample to use new perturb_path (untested)
Branches
issue-7
Mark Howison
graph: new pertub_path() for transcripts (untested)
Branches
issue-7
Mark Howison
graph: contigs() selects all paths through active graph (untested)
Branches
issue-7
Mark Howison
sampler: added RSEM abundance to likelihood calculation
Branches
issue-7
Mark Howison
debruijn: now takes Chrysalis debruijn graph as input instead of FASTQ
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
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