Releases: pachterlab/splitcode
v0.30.0
- Crucial bug fixes with tag identification including issue #11 and also another issue with using maxFindsG not behaving properly (i.e. tag identification terminating early) when maxFindsG is not set for certain tags.
- Add --unmask feature (an auxiliary feature) to take in two FASTA files (one masked and one unmasked) and extract the sequences that were masked.
- New extraction feature: Can do ^...^ to prepend a sequence to a UMI-like extraction pattern or ^^...^^ to append a sequence. E.g. <^AG^umi> means prepending AG to umi when it is extracted.
v0.29.4
- Allow outputting BAM files via --out-bam
- Updated QC (counts for each tag for each error distance outputted in summary file).
- Updated the column names to use singular words (i.e. tag instead of tags, group instead of groups, etc. -- though the plural version still works for backwards compatibility purposes).
- Allow keep:, keep-grp:, remove:, remove-grp: to be supplied directly in config file
- --keep-r1-r2 option to allow demultiplexing to be outputted using _R1.fastq and _R2.fastq suffixes (rather than _0.fastq and _1.fastq)
- Implemented a --min-delta
v0.29.3
v0.29.2
Changed 32-bit int to 64-bit int when getting number of mapped reads to avoid overflow when displaying progress of how many reads have been mapped. Resolves issue #8
Fixed specifying @no-chain in the config file (previously, it was not being recognized). Thanks to @bentyeh for pointing out this bug.
Allow no-chain to take in arguments about what should be chained vs not chained (e.g. specifying @no-chain x,y means no-chain only applies to the extraction/UMI-like string named x and the extraction/UMI-like string named y; others will still be chained together during the extraction).
Contributors
Assets 4
v0.29.1
v0.29.0
v0.28.6
v0.28.5
Only update in this release: when using minFinds or minFindsG without --assign, the reads that don't mean the min finds criteria will be thrown out (previously, without --assign, those options didn't do anything unless the keep or discard options were supplied).