Changes in version 1.1.3 - Fixed bug in smart-seq2 pileup_cells reporting Changes in version 1.0.0 - raer added to the Bioconductor project Changes in version 0.99.12 - Changes made to prepare for bioc submission Changes in version 0.99.11 - Replaced base R fisher test with c-wrapper to call htslib fisher test, which speeds up execution many fold. Changes in version 0.99.10 - The options to write to tabix indexed output files have been removed from pileup_sites() as they have limited utility and introduce unwanted code complexity. Changes in version 0.99.9 - The genomic-unstranded option for the library-type argument in FilterParam() has been renamed to unstranded, and the unstranded option has been removed. Changes in version 0.99.8 - Function arguments involving a fasta file have been renamed to all be fasta Changes in version 0.99.7 - added a single cell specific AEI calculation (calc_scAEI()) Changes in version 0.99.6 - added method to count base consensus base when counting UMIs with pileup_cells() using the sum of base qualities to select consensus. Changes in version 0.99.5 - 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. Changes in version 0.99.4 - 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. Changes in version 0.99.3 - support BamFile and BamFileList inputs to pileup_sites() and pileup_cells(), which provides an option to provide custom BAI index file names. Changes in version 0.99.2 - rename prep_for_de() and perform_de() to make_de_object() and find_de_sites(). Changes in version 0.99.1 - 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 Changes in version 0.99.0 - 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: - bed indexing (indexBed and related C code) - bam tag indexing (build_tag_index, show_tag_index, get_tag_bam, ) - bam tag index based single cell approach (sc_editing) - bam tag indexing C code from bri (src/bri/*) - sparse matrix merging for merge_pileups(). - unneeded utilities (filter_by_coverage) - Remaining (and mostly unused) Rcpp code - Removed fastmap, Rcpp, zlibbioc, RColorBrewer, and BiocGenerics dependencies - Removed system requirements for C libraries used by bri - 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.