New features in this version
- TAPS support in combination with other protocols, stable for NLAIII, experimental for scCHIC
- Tabulation tool for TAPS data
- Tagger for TAPS data
- Automated separation of DNA and RNA reads from a single cell
- Undigested site counting for digestion sequencing
- Feature annotation for molecules (genes/introns/exons/..)
- Sparse scanpy compatible count table generation
- HTML representation of molecules and fragments
- Tensor representation of molecules for machine learning applications
- It is now possible to use Custom QueryFlaggers, which allows for using BAM files which have custom information, for example cell barcode or UMI encoded in the read name.
- Variant masking in reference Fasta file
- binning utils module
- methods to extract cell barcode from molecule
- len() to fragment which returns the amount of associated reads
- Use R1/R2 primer lengths from fragment in span calculation
- add_readgroups_to_header function and sort_and_index function
Library statistics:
- CSV summary files containing diagnostics information
- Summary plots for methylation data
Fixes and improvements
- Load allele information more efficiently and cache informative variants
- Read and write gzipped GTF files
- Added show_read1/2 arguments to fragment to only visualise a single read
- Use hash descriptor for fragments for faster pooling to molecules
- Added requirements.txt
- Count table: do not count outside chromsome bounds when using sliding window
- Use the duplicate bam bit to decide if a fragment is duplicate instead of our own tags
- Check if reads are mapped before counting deduplicated reads
- Generated a list of used tags
- Updated mapping quality histogram
- Fixed base calling phred score calculation
- Allele_resolver is now an optional argument for Molecule
- do not use non-proper paired reads in the size histogram
- count and show amount of informative variants for the requested alleles. (allele resolver)
- demux.py now processes every input fastq file in a separate cluster job
- Added --nochunk flag which disables running a job per lane (demux.py)
- Don't raise exception when trying to visualise base aligned outside view (HTML view)
- readcount plot width has been reduced
Tests
- more tests for molecule pooling
- iterator_stability tests
- test_contig_selection test
- count table per chromosome test