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ISOFOX: integrate tars support (AUS-418) - #845

Merged

charlesshale merged 74 commits into

AUS418-isofox-tars

Sep 24, 2026

Commits on Jul 8, 2026

support tars alignments via XA multimap fan-out and 60 single-map MAPQ (AUS-418)
shiv-hartwig
committed
4637f80
Isofox: support tars alignments via XA multimap fan-out and 60 single-map MAPQ (AUS-418)
shiv-hartwig
committed
b83d6c7

Commits on Jul 13, 2026

base multimapper detection on XA loci and drop STAR references (AUS-418)
shiv-hartwig
committed
cbdab7b
Isofox: base multimapper detection on XA loci and drop STAR references (AUS-418)
shiv-hartwig
committed
725306d
minor nits addressed
shiv-hartwig
committed
bfe5b41
Isofox: minor nits addressed
shiv-hartwig
committed
a3ab8f4
rename LOW_MAP_QUAL fragment type to MULTI_MAPPED (AUS-418)
shiv-hartwig
committed
2642df0
Isofox: rename LOW_MAP_QUAL fragment type to MULTI_MAPPED (AUS-418)
shiv-hartwig
committed
797a746

Commits on Jul 14, 2026

Commits on Jul 15, 2026

clean up
shiv-hartwig
committed
2d76312
Isofox: clean up
shiv-hartwig
committed
29de024

Commits on Jul 21, 2026

Commits on Jul 24, 2026

Isofox:
shiv-hartwig
committed
2babc13

Commits on Jul 28, 2026

Isofox: rename LowMapQualFrags to MultiMappedFragments & record multi-mappers for tars
shiv-hartwig
committed
211d50c

Commits on Aug 17, 2026

Isofox: fusion check for position adjustment from junction base overlap
charlesshale
committed
eaa7c7b

Commits on Aug 26, 2026

Isofox: fix junction position adjustment and splice bases
shiv-hartwig
committed
b47121d

Commits on Aug 28, 2026

Isofox:
charlesshale
committed
c4c9f34
Isofox: fusion adjust split junc position from overlap with with known splice awareness
charlesshale
committed
89f0167

Commits on Aug 31, 2026

Commits on Sep 1, 2026

Commits on Sep 3, 2026

Commits on Sep 11, 2026

Commits on Sep 14, 2026

Isofox: fusion supporting fragments include junction and discordant, not realigned
charlesshale
committed
cad084d
Isofox: fusion soft-clips reads no longer have a max bases of 10
charlesshale
committed
2cc6033
Isofox:
charlesshale
committed
bfa9878

Commits on Sep 15, 2026

Commits on Sep 16, 2026

Isofox: remove proper pair condition for chimeric test, trim adapters based on matched alignment positions, not read ends
charlesshale
committed
257c6e8

Commits on Sep 17, 2026

Commits on Sep 18, 2026

Isofox: read caches and uses BAM record directly to avoid copying member data
charlesshale
committed
bf2fa28

Commits on Sep 19, 2026

Commits on Sep 20, 2026

Isofox: converted more writers to tsv output
charlesshale
committed
86cae28
Isofox: dropped chimeric read writing
charlesshale
committed
83718fc

Commits on Sep 22, 2026

Isofox: minor fixes
shiv-hartwig
committed
1c34ad2
Isofox: minor clean-ups and fixes
charlesshale
committed
67c4547
Isofox: resolved conflicts
charlesshale
committed
b8ef35d

Commits on Sep 23, 2026