v0.31.2

Minor update:

Besides allowing <~...> to reverse complement a sequence in "extract", can now use <c...> to simply complement a sequence and <r...> to simply reverse a sequence.

v0.31.1

Minor update to efficiency of read processing

v0.31.0

• Implemented --lift for creating genomes from VCF files and extracting sequences around variants and splice junctions
• Resolve issue #27 about a missing include
• Trying out an implementation of #24 (nested/secondary config files)
• Implemented issue #23 (reverse complement "revcomp" option for tag matching)
• Trying out an implementation of #22 (--from-name: extracting sequences from read names)
• Implemented #19 (--random)
• Fix #15 (JSON output having a trailing comma)
• zlib-ng enabled by default
• barcode-encode for hashing a sequence of barcodes to a unique nucleotide sequence

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

Allow spaces in arguments (e.g. config file name can have spaces in it)

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).

v0.29.1

Added --bclen= option to allow assigned final barcodes to be short or longer (of lengths 2 through 31), rather than just of length 16.

v0.29.0

New features and bug fixes: #5 and #6

v0.28.6

Fixed a critical bug when a config file has tags of different lengths and some tags were not being identified