pileup_sites() as they have limited utility and introduce unwanted code complexity.genomic-unstranded option for the library-type argument in FilterParam() has been renamed to unstranded, and the unstranded option has been removed.fastacalc_scAEI())pileup_cells() using the sum of base qualities to select consensus.pileup_cells() now allows for multiple alleles to be queried at a site.
Fixed an indexing bug in pileup_cells() that misassigned sites to counts.
annot_snps will now compare the site allele to the SNP allele and return a
column snp_matches_site indicating if the site matches the snp.
added new function, find_scde_sites() to identify differentially editing
sites in single cell data using fishers exact tests.
pileup_cells now respects the min_depth and min_variant_reads FilterParameters.
BamFile and BamFileList inputs to pileup_sites() and pileup_cells(), which provides an option to provide custom BAI index file names.prep_for_de() and perform_de() to make_de_object() and find_de_sites().default values for edit_from and edit_to for calc_edit_frequency() have
been changed to A and G respectively.
renamed type argument in perform_de to test and removed type argument in
prep_for_de
added support for processing multiple BAM files with calc_AEI().
Dropped minimally used bad_reads and reads parameters from pileup_sites()
Added utility to screen scRNA-seq bam files for regions with oligo-dT mispriming (find_mispriming_sites()).
add option to query ref and alt SNP alleles
added tests for SummarizedExperiment filtering approaches
added a strand bias stat sor using approach from GATK (StrandOddsRatio), and
a confidence score calc_confidence() from SAILOR pipeline.
'N' bases in read or reference are ignored
Removed outdated or unused functionality:
indexBed and related C code)build_tag_index, show_tag_index, get_tag_bam, )sc_editing)src/bri/*)merge_pileups().filter_by_coverage)The bed indexing used in pileup_sites() has been replaced with the region indexing approach from pileup_cells().
pileup_sites() now requires a GRanges object rather than a bed file. The bedfile parameter has been removed and replaced with a sites parameter.
Renamed Ref and Var output columns to REF and ALT and nVar was renamed to nAlt. This provides consistency with VCF format and consistency across pileup_cells() and pileup_sites() function calls
pileup_cells() gained functionality to process multiple smart-seq2 style bam files.
Changed filterParam argument in pileup_sites and pileup_cells to param for simplicity.
Added FilterParam to exclude multi-allelic sites report_multiallelic, or exclude reporting a variant in the Var assay based on allelic frequency (min_allelic_freq).
The bam_flags parameter used in pileup_sites and pileup_cells has been moved into the FilterParam class.
The bedindex parameter for pileup_sites has been removed. This option is not needed
at the user level and is planned to be replaced by the regional indexing used in pileup_cells().
Added FilterParam option to trim reads based on fractional distance from 5' (ftrim_5p) or 3' end (ftrim_3p).
Incorporated RBPZ and VDB statistics from bcftools, now returned as rowData columns
when calling pileup_sites.
A RangedSummarizedExperiment object is now directly returned from pileup_sites. Using merge_pileups is no longer necessary and is not an exported function.
Renamed get_pileup to pileup_sites and create_se to merge_pileups
Rename remove_clustered_variants, remove_multiallelic, and remove_splice_variants
to filter_* for consistency.
Rewrote and renamed the single cell editing function sc_editing to pileup_cells(). pileup_cells() does not require sorting and index by cell barcode, uses a new format to specify sites to query and requires providing the reference and alternate alleles of interest, writes to disk in a sparse matrix compatible format to reduce memory usage, and should have more performance as there is no need to query a fasta index.
Implemented method to collapse reads with duplicate UMIs.
Added option to filter sites in pileup based on number of reads containing a variant (#54)
Added a NEWS.md file to track changes to the package.