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ablab / IsoQuant Public

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Issues 53
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Merge single cell functionality into main branch#360

Merged

andrewprzh merged 204 commits intomasterablab/IsoQuant:masterfrom

sc_3.10ablab/IsoQuant:sc_3.10Copy head branch name to clipboard

Dec 23, 2025

Conversation Commits204 (204)Checks Files changed

Merged

Merge single cell functionality into main branch#360
andrewprzh merged 204 commits intomasterfrom
sc_3.10

Commits

Commits on Dec 22, 2025

add barcode calling, single file only
andrewprzh
committed
fix barcode calling execution
andrewprzh
committed
split barcodes by chromosomes
andrewprzh
committed
minor aggregator refactoring
andrewprzh
committed
fix requirements
andrewprzh
committed
minor refactoring of UMI filtering
andrewprzh
committed
score for double barcode calling
andrewprzh
committed
fix imports for now
andrewprzh
committed
load barcodes with score
andrewprzh
committed
proper usage of UMIFilter
andrewprzh
committed
report some stats while filtering
andrewprzh
committed
fixes
andrewprzh
committed
fix naming
andrewprzh
committed
add umit filtering to isoquant pipeline
andrewprzh
committed
FIX BUG
andrewprzh
committed
fix option
andrewprzh
committed
fix stats
andrewprzh
committed
fix clearing
andrewprzh
committed
fx unique
andrewprzh
committed
do not skip reads in stats
andrewprzh
committed
fix imports
andrewprzh
committed
do not ignore non-unique in stats counting
andrewprzh
committed
report spliced reads
andrewprzh
committed
do all distances
andrewprzh
committed
fix imports
andrewprzh
committed
skip barcode calling in the resumed run
andrewprzh
committed
fix --resume in sc mode
andrewprzh
committed
argv in main
andrewprzh
committed
array based index
andrewprzh
committed
set default k=6
andrewprzh
committed
ignore secondary in barcode calling
andrewprzh
committed
fx imports
andrewprzh
committed
allow multiple files for barcode calling
andrewprzh
committed
enhance allinfo
andrewprzh
committed
proper attribute output
andrewprzh
committed
Barcode calling: handle gzipped read assignment file, correct number of columns

almiheenko
authored and
andrewprzh
committed
Add editdistance to requirements

almiheenko
authored and
andrewprzh
committed
thread barcoded reads properly
andrewprzh
committed
move barcode caller into root
andrewprzh
committed
simple read info
andrewprzh
committed
create barcode callers within each thread
andrewprzh
committed
log
andrewprzh
committed
read storage class
andrewprzh
committed
do not duplicate headers
andrewprzh
committed
do not forget header in single thread
andrewprzh
committed
do not clear chunks
andrewprzh
committed
switch from non-lazy ProcessExecutorPool.map to self-made asynchronous lazy iteration
andrewprzh
committed
run barcode calling in a separate process due to memory issues with GC
andrewprzh
committed
cosmectics
andrewprzh
committed
fx
andrewprzh
committed
comment explaining separate process for barcode calling
andrewprzh
committed
allow gzipped barcodes
andrewprzh
committed
proper exception handling
andrewprzh
committed
fix chunk size
andrewprzh
committed
propose a more elegant version for the future
andrewprzh
committed
experimental extraction, if the last bases of primer are not aligned, still consider them as aligned and not use barcode right afterwards
andrewprzh
committed
fix delta 0
andrewprzh
committed
use annotated polyA sites for reported polyA sites within 50 bp
andrewprzh
committed
stereo
andrewprzh
committed
fix
andrewprzh
committed
count multiple linkers in stereo mode
andrewprzh
committed
fix stat
andrewprzh
committed
fix
andrewprzh
committed
report empty
andrewprzh
committed
more stats
andrewprzh
committed
fix iterative linker search
andrewprzh
committed
load h5 barcodes
andrewprzh
committed
fix decoding
andrewprzh
committed
improve h5 loading
andrewprzh
committed
2bit indexing
andrewprzh
committed
implement stereo barcode calling
andrewprzh
committed
old function
andrewprzh
committed
2bit indexing for stereo
andrewprzh
committed
fx import
andrewprzh
committed
do not output large UMIs
andrewprzh
committed
fix barcode extraction and score
andrewprzh
committed
try to reduce the number of SW calls
andrewprzh
committed
do not scan read multiple times for now
andrewprzh
committed
fix minscore logic
andrewprzh
committed
minor fixes for primer
andrewprzh
committed
fix output
andrewprzh
committed
use untrusted UMIs but only when trusted are not present
andrewprzh
committed
add stereo mode
andrewprzh
committed
include stereo mode, improve output naming
andrewprzh
committed
use k=14 for stereo
andrewprzh
committed
read de-concatenation with TSO search
andrewprzh
committed
draft for splitting barcode caller
andrewprzh
committed
improve printing
andrewprzh
committed
use multiple files for umi filtering
andrewprzh
committed
fix .gz
andrewprzh
committed
fix untrusted UMI filtering
andrewprzh
committed
one more filtering fix
andrewprzh
committed
properly deconcatenate reads, do not print non-informative results
andrewprzh
committed
debug mode
andrewprzh
committed
fix non splitting stereo barcode detector
andrewprzh
committed
print *, relax ED cutoffs, try to speed up some searches in bigger string chunks
andrewprzh
committed
output FASTA in a proper way
andrewprzh
committed
stats
andrewprzh
committed
ensure the step is always made
andrewprzh
committed
print empty result
andrewprzh
committed
embed read splitting into the pipeline
andrewprzh
committed
umi ed for different modes
andrewprzh
committed
factor out assignment loading
andrewprzh
committed
properly process ambiguous reads
andrewprzh
committed
refactor umi deduplication, use raw assignments instead of parsing TSV files
andrewprzh
committed
perform umi filtering right after the assignment step
andrewprzh
committed
save umi-filtered reads to a save file
andrewprzh
committed
use umi filtered reads from counting and constuction
andrewprzh
committed
print more stats on duplicated molecules
andrewprzh
committed
back to normal indexing
andrewprzh
committed
output only sequences with TSO when splitted, more stats
andrewprzh
committed
try to speedup tso and linker look ups
andrewprzh
committed
fix split 0
andrewprzh
committed
fix None as assigned gene in allinfo files
andrewprzh
committed
update requirements
andrewprzh
committed
fix tenx caller
andrewprzh
committed
remove min score
andrewprzh
committed
fix imports for umi filtering
andrewprzh
committed
single array index
andrewprzh
committed
visium hd caller
andrewprzh
committed
polyA dirty fix
andrewprzh
committed
use iterators instead of list, split barcodes and other perfromance optimizations
andrewprzh
committed
fix modes
andrewprzh
committed
shared memory index implementation
andrewprzh
committed
unify modes and barcode calling
andrewprzh
committed
fix curio barcode detection
andrewprzh
committed
fix messages for stereo
andrewprzh
committed
fix args check
andrewprzh
committed
implement shared memory index in a nice way
andrewprzh
committed
unify single and multiple threads, minor refactoring and simplification
andrewprzh
committed
use output prefix, create outdir automatically
andrewprzh
committed
umi filtering parallel version
andrewprzh
committed
fix gene barcode pair stats, simpify check
andrewprzh
committed
fix resume logic
andrewprzh
committed
stereoseq no split parallel version, use usual k-mer idexer for low barcode count
andrewprzh
committed
fix dir creation
andrewprzh
committed
fix afer rebase, fix naming
andrewprzh
committed
more tests
andrewprzh
committed
even more tests
andrewprzh
committed
count ED in addition to score for visium calling
andrewprzh
committed
fix print
andrewprzh
committed
add check_sq to process unmapped bams
andrewprzh
committed
remove print
andrewprzh
committed
fix visium
andrewprzh
committed
minor usability fixes
andrewprzh
committed
fix typo
andrewprzh
committed
use score difference for non-exact mathes
andrewprzh
committed
fix second best score keeping
andrewprzh
committed
fix None
andrewprzh
committed
fix clean up and allinfo merging
andrewprzh
committed
--no_large_files
andrewprzh
committed
fix r2t
andrewprzh
committed
fix no_large_files and lock files
andrewprzh
committed
merge large files only when needed
andrewprzh
committed
proper --resume and sc pipeline interaction
andrewprzh
committed
add --barcode2spot option
andrewprzh
committed
do not split regions united by genes
andrewprzh
committed
merge consecutive genes
andrewprzh
committed
refactor varios binary read assignment loader, implement merging assignment loaders
andrewprzh
committed
fix unique gene-barcode pairs
andrewprzh
committed
sort molecules before detecting similar UMIs to avoid weird clustering
andrewprzh
committed
use umi length when prioritizing UMIs
andrewprzh
committed
fix diff function
andrewprzh
committed
use actual read count for sorting
andrewprzh
committed
filter out ambiguous gene assignments
andrewprzh
committed
fix empty set of filtered reads
andrewprzh
committed
parallel barcode table split
andrewprzh
committed
Support for multiple read groups
andrewprzh
committed
Fix BasicReadAssignment deserialization for list read_group
andrewprzh
committed
Use read_group[0] in counters (temporary fix)
andrewprzh
committed
Join read_group list in TSV output
andrewprzh
committed
use first group in model construction for now
andrewprzh
committed
Implement proper multi-group counters with strategy-based naming
andrewprzh
committed
Fix references to grouped counters (now lists)
andrewprzh
committed
Update test to expect new grouped file naming format
andrewprzh
committed
Fix multi-group support in GraphBasedModelConstructor
andrewprzh
committed
Fix technical replicas check to only use file_name group
andrewprzh
committed
fix tests
andrewprzh
committed
Auto-add file_name grouping when multiple files are present
andrewprzh
committed
set use_technical_replicas later
andrewprzh
committed
Make use_technical_replicas a per-sample property
andrewprzh
committed
cosmetics
andrewprzh
committed
Implement improved parallel table splitting algorithm
andrewprzh
committed
Replace chunked loading with line-by-line streaming for better efficiency
andrewprzh
committed
remove unused code
andrewprzh
committed
Add barcode/umi to ReadAssignment to eliminate redundant loading

andrewprzh
and
claude
committed
Add barcode_spot grouping to group reads by cell type/spot

andrewprzh
and
claude
committed
fix balancing
andrewprzh
committed
fix serialization and barcode split
andrewprzh
committed
refactor umi filtering, add type hints and remove unused code

andrewprzh
and
claude
committed
use barcodes from read assignments
andrewprzh
committed
fix stats
andrewprzh
committed
TODOs
andrewprzh
committed
remove ReadAssignmentInfo, use ReadAssignment.additional_attributes
andrewprzh
committed
remove unused barcode loading functions
andrewprzh
committed
document single-cell/spatial options, update read_group
andrewprzh
committed
more TODOs
andrewprzh
committed
fix imports
andrewprzh
committed
add stereo toy data test
andrewprzh
committed
add unit tests for UMI filtering and read groups
andrewprzh
committed
fix test imports and class names
andrewprzh
committed
add tests and comments
andrewprzh
committed
fix some tests
andrewprzh
committed
fix test signatures and remove duplicate functions

andrewprzh
and
claude
committed

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