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NEWS
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NEWS
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# 0.7.0
- Fix deprecation error in yaml
- Fix deprecation error in snakemake
# 0.6.9
- UMI parsing fix for `tenx` mode thanks to @yaniv-el
# 0.6.8
- Speedups for `tenx` mode thanks to @ruochiz
# 0.6.7
- Updates to deletion calling module
# 0.6.6
- Fix naming parameters in tags
- update `check` issue with tenx mode
# 0.6.4
- Allow for barcodes with ACGT but not the -n convention
# 0.6.3
- Facilitate CellRanger-ATAC v2 bam file
- Alpha version of remove-background
# 0.6.2
- Fixed bug associated with tenx mode
# 0.6.1
- Automated variant calling in python thanks to @vincent6liu
- Command line option to handle overlapping mate reads thanks to @vincent6liu
# 0.6.0
- Functionality for mgatk-del
# 0.5.9
- Fix bug in strand assignment in `(b)call` mode
# 0.5.8
- Fix (hopefully innocuous) bug thanks to @bobermayer
# 0.5.7
- Automatically generate .rds file for use with Signac
# 0.5.6
- Added `tenx` mode for more efficient processing of large single-cell datasets
# 0.5.0
- Beta version distributed via PyPi
- Revamped code used in mtscATAC-seq paper
# 0.4.0
- Fully separated by strand for counts / qualities
- UMI-based duplicate read removal available
- Default to remove PCR duplicates
# 0.3.9
- Handle common reference genome issue for human genomes (hg19 / rCRS) automatically
# 0.3.4
- Full support for `bcall` mode
# 0.3.0
- Per-base / allele quality scores
# 0.2.5
- Creates .rds for easy i/o into R package
- Efficient sparse matrices for final text-based output
- Added additional run modes. 5 total as of now (call, one, gather, support, check)
# 0.1.0
- Alpha version uploaded to PyPi
# 0.0.1
- Added NEWS