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Isofox changes for Ultima support (AUS-418) - #893

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shiv-hartwig wants to merge 29 commits into

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AUS418-isofox-ultima-refactor

Commits on Jun 19, 2026
- Esvee: removed private method only
  charlesshale
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  ad30f46
Commits on Jun 22, 2026
- Esvee: removed redundant code
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  238af7a
- Esvee: removed private method
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  17c222e
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
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  bdf6af9
Commits on Jun 23, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  6720c4d
Commits on Jun 26, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  dff3459
Commits on Jun 29, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
  committed
  18d9387
Commits on Jun 30, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  2eb5549
Commits on Jul 2, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  2a704c5
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
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  65d4ad6
Commits on Jul 13, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
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  0ddfcf8
Commits on Jul 15, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  1056453
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  eab6c69
Commits on Jul 16, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  82aa9a4
Commits on Jul 23, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  d526cba
Commits on Jul 26, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  a33829e
Commits on Aug 4, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  6235396
Commits on Aug 12, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  6e302b1
Commits on Aug 25, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  900df77
Commits on Sep 15, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
  committed
  adaddef
Commits on Sep 24, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  43ac458
Commits on Sep 29, 2026
- Merge branch 'master' of https://github.com/hartwigmedical/hmftools
  charlesshale
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  0a0a7db
- Isofox:
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  04babcb
- Isofox: fixed no setting genic data for chimeric primary reads
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  7f01342
Commits on Sep 30, 2026
- Isofox: added unit test for previous issue
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  f53d653
- Isofox: fusion passing filter test for short locals now requires dup-del orientations
  charlesshale
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  7cb017a
Commits on Oct 5, 2026
- Isofox: allow INV and BND discordant fragment support without requiring soft-clips
  charlesshale
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  7c0c786
Commits on Oct 6, 2026
- Isofox: add Fragment class and single-end read support (AUS418)
  shiv-hartwig
  committed
  6dfc453
- Isofox: fix README
  shiv-hartwig
  committed
  74700f3

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