Transcriptome polish - #649

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diekhans wants to merge 125 commits into

BrooksLabUCSC:devfrom

diekhans:transcriptome-polish

Commits on Mar 9, 2026

Commits on Mar 18, 2026

Merge branch 'transcriptome-polish' of github.com:diekhans/flair into dev
cafelton
committed

Commits on Mar 24, 2026

Commits on Mar 25, 2026

transcriptome: fix novel gene detection bug
cafelton
committed

Commits on Apr 2, 2026

fix SE gene detection bug, add polyA and intprim detection to indiv. reads
cafelton
committed
added polyA strand correction for single exon reads
cafelton
committed

Commits on Apr 4, 2026

transcriptome: fix novel gene detection bug

cafelton
authored and
diekhans
committed
add more fusion files, fix close genes on negative strand fusion filtering

cafelton
authored and
diekhans
committed
make combine options more intuitive

cafelton
authored and
diekhans
committed
stranding notes, also fixed bug in single exon gene identification (broke test-transcriptome-seg1)

cafelton
authored and
diekhans
committed
fix SE gene detection bug, add polyA and intprim detection to indiv. reads

cafelton
authored and
diekhans
committed
added polyA strand correction for single exon reads

cafelton
authored and
diekhans
committed
test is noew the default target
diekhans
committed
claude add doc
diekhans
committed
fixed flake8 errors after merge
diekhans
committed
added github workflow to fix flake8 errors
diekhans
committed
flake8 fixes
diekhans
committed
added FIXME to use samtools for filtering
diekhans
committed
work with Claude on fixing flake8 errors
diekhans
committed

Commits on Apr 5, 2026

Commits on Apr 7, 2026

Merge branch 'transcriptome-polish' of github.com:diekhans/flair into dev
cafelton
committed

Commits on Apr 9, 2026

add more fusion files, fix close genes on negative strand fusion filtering

cafelton
authored and
diekhans
committed
make combine options more intuitive

cafelton
authored and
diekhans
committed
stranding notes, also fixed bug in single exon gene identification (broke test-transcriptome-seg1)

cafelton
authored and
diekhans
committed
fix SE gene detection bug, add polyA and intprim detection to indiv. reads

cafelton
authored and
diekhans
committed
update args in count_sam_transcripts

cafelton
authored and
diekhans
committed
fix flake8 in count_sam_transcripts

cafelton
authored and
diekhans
committed
set strand based on gene when matching transcriptome
diekhans
committed
resolved merge issues
diekhans
committed
merge some merge mistakes
diekhans
committed
added back check for no support loaded
diekhans
committed

Commits on Apr 11, 2026

remove uncessary re-creation of a BED during junction correction
diekhans
committed

Commits on Apr 14, 2026

Commits on Apr 15, 2026

add definition of old direct-RNA
diekhans
committed

Commits on Apr 19, 2026

cleanup up of count_sam_transcripts
diekhans
committed

Commits on Apr 20, 2026

mior optimzation of cigar parsin
diekhans
committed

Commits on Apr 22, 2026

fixed potential multiprocessing issues with error handling
diekhans
committed

Commits on Apr 23, 2026

Commits on Apr 24, 2026

switch from IntervalTree to ruranges_py to speed up intron support
diekhans
committed

Commits on Apr 28, 2026

wrap execution of count_sam_transcripts in a function to abstract calling a program.
diekhans
committed

Commits on May 6, 2026

Commits on May 11, 2026

update predictProd to work with additional columns in bed file
cafelton
committed

Commits on May 12, 2026

Commits on May 14, 2026

change gene ID handling to use hashes, clean up final IDs
cafelton
committed

Commits on May 15, 2026

Commits on May 18, 2026

Commits on May 19, 2026

Commits on May 20, 2026

Commits on Jun 5, 2026

restore correct behavior of checking poly(A) as htslib has already oriented the reads
diekhans
committed