v0.31.6

• Preserve quality scores when doing --extract (issue #18 )
• --extract can be specified multiple times on the command-line (issue #42 )
• Automatically create output directories if they don't exist (issue #41 )
• Update cmake minimum version to 3.10
• Hopefully finished resolving a race condition in issue #45

v0.31.5

What's Changed

• Merge 0.31.5 into main by @Yenaled in #52

Full Changelog: v0.31.4...v0.31.5

A bug-fix release: Issues #51 #49 #47

v0.31.4

Attempt to resolve race condition issue with QC/summary in issue #45
Be more flexible with filenames in --keep (e.g. allow spaces, allow custom-defined files) per issue #44
Keep BAM file pairing when using --select with exactly two files per issue #39
Release fixes hashmap overflow issue (by enabling C++17 whenever possible) per issue #37
Added sub-barcode-encode feature, enabling specifying barcodes [a][b][c][d][e] and a sub-barcode [c][d][e] to be separately encoded into the final barcode.

v0.31.3

Fixes issue #33
Fixes bug with barcode-encode when setting barcode-encode in config file (issue #34 )

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)