AUS419 purple ffpe by charlesshale · Pull Request #885 · hartwigmedical/hmftools

charlesshale · 2026-09-15T04:02:55Z

Purple:

added resegmentation routine for FFPE, runs for WGS only

Linx:

disruption drivers use likelihood 1 if undisrupted copies < 0.5

Multiple tools:

check driver gene names against Ensembl

… issue

- removed unused gc_profile config - handle (rare) driver event on short arm CN look up

…for Ensembl driver gene name tests

charlesshale added 30 commits June 19, 2026 12:37

Esvee: removed private method only

ad30f46

Esvee: removed redundant code

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Esvee: removed private method

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Merge branch 'master' of https://github.com/hartwigmedical/hmftools

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Merge branch 'master' of https://github.com/hartwigmedical/hmftools

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Merge branch 'master' of https://github.com/hartwigmedical/hmftools

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Merge branch 'master' of https://github.com/hartwigmedical/hmftools

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Merge branch 'master' of https://github.com/hartwigmedical/hmftools

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Merge branch 'master' of https://github.com/hartwigmedical/hmftools

2a704c5

Merge branch 'master' of https://github.com/hartwigmedical/hmftools

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Merge branch 'master' of https://github.com/hartwigmedical/hmftools

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Merge branch 'master' of https://github.com/hartwigmedical/hmftools

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Merge branch 'master' of https://github.com/hartwigmedical/hmftools

eab6c69

Merge branch 'master' of https://github.com/hartwigmedical/hmftools

82aa9a4

Merge branch 'master' of https://github.com/hartwigmedical/hmftools

d526cba

Merge branch 'master' of https://github.com/hartwigmedical/hmftools

a33829e

Purple: clean-up only

b130e20

Purple: resegmentation calc penalty

5c1ae6a

Purple: added resegmentation routine

ffd8f6c

Purple: added resegmentation tests

e902948

Linx: disruption drivers use likelihood 1 if undisrupted copies < 0.5

22a6e32

Purple: minor refactors to resegmentation

b12e8ce

Purple: reseg set merged regions field use baf and depth weights

8ee1244

Purple: reseg blend final diploid regions

864c66a

Purple: reseg fixed aggregate diploid region obs tumor ratio and BAF

394dce2

Purple: reseg handle null primary peak

b3075cf

Purple: reseg minor change to blending

78c573b

Purple: reseg do gc norm before calculating penalty

0875abf

Linx: fixed max del and dup length getters

439ebc6

Linx: fixed another ref to long dup cut-off length in clustering

0733912

charlesshale added 10 commits August 20, 2026 16:30

Linx: code clean-up only

d6724ac

Linx: version to 2.4

068e1a1

Purple: resegmentation on by default for non-panel, fixed minor reseg…

8eab3fa

… issue

Purple:

7b85c18

- removed unused gc_profile config - handle (rare) driver event on short arm CN look up

Purple: reseg minor fix for handling skipped regions

4f6eb7f

Common: Ensembl cache data files now expect ref genome version in name

9331a15

Common: ensembl data file loading checks for old filename

c8e7479

Purple, Linx, BamMetrics: check driver gene names against Ensembl

7a365fa

Sage: check driver gene names against Ensembl

49187ba

Merge branch 'master' into AUS419-purple-ffpe

aa2ac49