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Merging Battenberg v2.2.9 #47

Merged
merged 70 commits into from
Apr 2, 2020
Merged

Merging Battenberg v2.2.9 #47

merged 70 commits into from
Apr 2, 2020

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sdentro
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@sdentro sdentro commented Apr 2, 2020

  • Rewrite of GC correction code
  • Inclusion of replication timing correction
  • Inclusion of SV breakpoints made easier
  • Increased decimal precision
  • Various bug fixes
  • Extended README

sdentro and others added 30 commits July 29, 2018 12:46
@sdentro
Speeding up creation of logRsegmented by splitting large data frames
2e4f547
@jdemeul
Merge pull request #1 from Wedge-Oxford/master
3975a29 
Update master with upstream Wedge-Oxford
@jdemeul
rewrite of WGS GC correction including replication timing
555a73a
@jdemeul
update wrapper functions and example
34d213c
@jdemeul
omit reading in larger windows
6d41af9
Updating ASCAT dependency from 2.5 to 2.5.1
2c4544d
Updating Dockerfile to new version of allelecount
bfb71b5
Adding fix for an error thrown during creation of the sunrise plot. p…
25aba16 
…lot will still be made, but without the X
@sdentro
added fix from @jdemeul from pull request 27 without the extra commit…
a5d6f51 
…s from various merges
@sdentro
Merge branch 'dev' of https://github.com/sdentro/battenberg into dev
7c5b404
@kzkedzierska
Fixed the regex out of dev branch
8ec951e
@sdentro
Merge pull request #33 from kzkedzierska/regex_fixed
a8e8bb8 
Fixed the regex out of dev branch
@sdentro
Updating dockerfile to contain pipeline dependencies
bb01461
@sdentro
Adding update to Docker installation instructions and a description o…
0a1bd78 
…f the subclones.txt file contents. output file descriptions should be further extended and improved in the future
@sdentro
previous update detached header from section, now resolved
3db28fe
@sdentro
Adding separate allele counting pipeline
cf55cc6
@sdentro
Spelling
62fa42b
@sdentro
Updating README
58f818e
@sdentro
Added grch38 decription to readme
402701d
@sdentro
Clarify Docker reference data
ffb1d10
@sdentro
Fixed crash when creating haplotyping plot after no phasable SNPs wer…
8b8d21c 
…e found
@sdentro
Fixed typo
87dfa36
@sdentro
setting scipen to 999 upon loading the package, fixing scientific not…
7ab5888 
…ation in output files
@sdentro
Adding script to produce breakpoints from BRASS calls
a326d3f
@sdentro
Merge branch 'dev' of https://github.com/sdentro/battenberg into dev
b790d12
@sdentro
Update dockerfile to place sv script
4a0a769
@sdentro
add missing command line parser arguments to allelecount script
bcb37b0
@sdentro
Upgrade command line interface of the WGS pipeline and adding option …
e6e4cc6 
…to supply prior breakpoints
@sdentro
Merge pull request #31 from jdemeul/gc-replication-correct
68b8dd8 
Rewrite WGS GC correction including replication timing
@sdentro
Moved parsers into util and replaced a few calls to read.table and re…
264d502 
…ad_table_generic
sdentro added 29 commits May 23, 2019 21:13
@sdentro
fix placing scripts in dockerfile
73ac068
@sdentro
make sure brass breakpoints always have a column header
d8050a7
@sdentro
catch case when there is no clonal CNA called
06ed359
@sdentro
Add first copynumber profile to tarball
e14bc8f
@sdentro
Merge pull request #36 from Wedge-Oxford/new_gc_correction_testing
921e33d 
Upgraded GC content correction incorporated and tested
@sdentro
add splines dependency
3a624c7
@sdentro
Updating documentation
eec547b
@sdentro
update documentation
7362591
@sdentro
update version
b21cc76
@sdentro
Update paths to reference files
224f657
@sdentro
Catch case where recalculating psi_t yields an NA. This is rare and o…
81fa8d9 
…ccurs only when no segment could be fit with a clonal state given the found purity
@sdentro
Check if imputeinfo files exist
2e6c155
@sdentro
Changed default segmentation function to what was previously segment.…
c18f24a 
…baf.phased.sv and marked segment.baf.phased.sv as deprecated. Moved old segment.baf.phased to segment.baf.phased.legacy and removed the step where the median was BAF per segment was used to revert it back to original functionality.
@sdentro
Adding new default segment summary option no 3. This takes the median…
d0c419a 
…, unless the median equals 0 or 1 when the mean is taken. This choice is made per segment
@sdentro
Setting default segmentation summary to option 3
6534692
@sdentro
now reading in prior breakpoints within the segmentation function
ef32e7a
@sdentro
Merge branch 'dev' of github.com:Wedge-Oxford/battenberg into dev
f37dff5
@sdentro
Commenting out now deprecated sv segmentation function
dadbc87
@sdentro
replace ifelse with regular if when loading prior breakpoints
b8b092c
@sdentro
propagating prior_breakpoints to callSubclones to include these in th…
df7822c 
…e final plots
@sdentro
Refactoring some variable names and code cleanup
bf9057c
@sdentro
Further refactoring, changing variable names to be consistent
0e016d3
@sdentro
Adding new segment summary option to the merge_segments function in c…
add077d 
…allSubclones and some extra docs
@sdentro
Remove erroneous bracket
6f40291
@sdentro
Updating documentation
865bba1
@sdentro
Adding section about SV filtering to readme
e5369b0
@sdentro
Improve installation instructions
e323ab2
@sdentro
Formatting fix
aa171fc
@sdentro
Extend dependencies description
1bdf005
@sdentro sdentro merged commit 8bfb278 into master Apr 2, 2020
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3 participants
@sdentro @jdemeul @kzkedzierska