Singlecellmultiomics

This version contains a fix for a bug which caused QC-failed reads to sometimes get lost when multi-threading is enabled. Valid reads were not affected.

Contains many updates from 2020 and Jan 2021

Version bump.

All barcode files now start at index 1
BamTabulator: show available tags and pysam attributes
Added -max_handles setting to bamSplitByTag.py
Index bams using multiple threads
Added overseq count table generator
Extended help and added blacklist argument
Added functions to read and write blacklist to bam file header
Added timeout args
Write blacklisted regions to bam file
Change default strand inversion value
Use -p flag for samtools merge to prevent PN: dupes
Fall back on calling samtools binary, it works better with -c -p flags
Added gitignore folders
Added XA filter to bamFilter
Check validity of —contexts_to_capture
Fixed taps strand parameter bug, set taps strand default to R
Fix out of range error when using contexts_to_capture and molecule is on start of contig

This release contains a bugfix which resolves molecules being under or over counted when using `bamToCountTable.py --dedup`



BuysDB (49):
Added 3bp context profiler
Added annotated chic molecule tagging method
Added consensus options to multiprocessing
Added context extraction method
Added covariate extraction methods
Added covariate_key generator
Added customisable offset for wig export
Added custom methylation contexts
Added DS-methylation extraction script
Added no-qcfail flag
Added prob_to_phred method
Added --r1only to chic workflow
Added recalibration functions
Added simple mutation profiler
Added -tagthreads parameter to control how many threads are used for tagging
Add options and tests to only count R1, or R2
Always use both mates
Check for min_mq not being defined
Check if all files are indexed
Cleaned up code and added examples
Clean up handles to prevent memory leaks
Clean up labels
Clip output confidences to 0-62 phred range
Close plots to reduce memory footprint
Create plots and aggregate by strand and mate
Fixed tag descriptions
Fix phred score calculation
Improved handling when passing over deletions. Refactoring
**Never count half counts on properly formatted bam files**
optimisations, do not perform pileups in single bp binsize mode, perform pruning in thread.
Parameter passing fixes, and dealing with some globals
Properly import the indexing function
Psuedoread super call
Raise error when wrong fasta file is supplied
Refactoring
Removed DS check, added verbosity flag, fixed indentation
Removed required reference path
Renamed bamFileTabulator in Readme to bamTabulator
Revert to mean normalisation when median fails
Run on a single node for slurm (-N 1)