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Changelog

Source: NEWS.md

raer 1.1.3

  • Fixed bug in smart-seq2 pileup_cells reporting

raer 1.0.0

  • raer added to the Bioconductor project

raer 0.99.12

  • Changes made to prepare for bioc submission

raer 0.99.11

  • Replaced base R fisher test with c-wrapper to call htslib fisher test, which speeds up execution many fold.

raer 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.

raer 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.

raer 0.99.8

  • Function arguments involving a fasta file have been renamed to all be fasta

raer 0.99.7

  • added a single cell specific AEI calculation (calc_scAEI())

raer 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.

raer 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.

raer 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.

raer 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.

raer 0.99.2

raer 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

raer 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 bedfileparameter 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.