NEWS

# 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