Single-cell I/O: compress intermediates, add tagged and deduplicated BAM outputs - #421

Open

andrewprzh wants to merge 18 commits into

Commits on Aug 24, 2026

gzip split reads fasta unless --no_gzip
andrewprzh
committed
2e4b2cd
compress barcode tables when the run finishes
andrewprzh
committed
1edc313
Add tagged_bam and deduplicated_bam large outputs
andrewprzh
committed
1cb06dd
document tagged and deduplicated BAM formats
andrewprzh
committed
d2cc650
warn at startup when a BAM output cannot be produced
andrewprzh
committed
213aa05
do not use deduplicated bam for fusion detection
andrewprzh
committed
e844fad
cover all references and unmapped reads in tagged bam
andrewprzh
committed
3c2596e
fix tagged bam docs to match full reference coverage
andrewprzh
committed
d9e3508
abort when splitting is requested for aligned input
andrewprzh
committed
163aafd
merge bam fragments in batches to stay under the open file limit
andrewprzh
committed
80bce9a
compress new single-cell outputs at gzip level 6
andrewprzh
committed
d1e226a
derive the tagged bam reference list once and split barcodes to matching paths
andrewprzh
committed
1691518
do not rebuild the tagged bam on resume
andrewprzh
committed
4b6983b
fix split reads fasta name in the standalone tool docs
andrewprzh
committed
9dea1a9
record real-data gzip level measurements
andrewprzh
committed
ecbad06
compress FASTA output at gzip level 4 and route all gzip writers through the shared helper
andrewprzh
committed
7b47376
keep barcode calling output order independent of chunk completion order
andrewprzh
committed
0a9a03a

Commits on Aug 25, 2026

note that the gzip timestamp is left alone
andrewprzh
committed
53f943e