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.