v4.1.0

• Change: --length-range default change from 50:500 to 30:999999.
• Feature: HardClipEnd: new process to hard remove the last N bases.
• Change: names in processing order (--order -O) changed.
• Feature: PCRDedup: remove PCR duplicates from fastq files. The entire paired sequence is compared and hashed. This method require large memory because it stores hashes of reads. To enable, use --pcr-dedup.
• Feature: processing stats are recorded in the json file.
• Fix: polyX_tail_scan algorithm now is more precise, and tailing Ns also count.

v4.0.3

• Fix: --order or -O option should accept multiple arguments.

v4.0.2

v4.0.2

• Fix: --detect-adapter for paired reads: refer to index 1 of empty vector when no adapter is found.

v4.0.1

v4.0.1

• Fix: dep cihga39871/BioSequences.jl: detailed error message if input files' line break is '\r\n'.

v4.0.0

• Optimize: algorithm: now the non-overtrim rate for reads without adapters are higher.
• Feature: re-write trimming to allow trim multiple adapters at the same time. This change is adjusted for metabarcoding data.
• Feature: hard-clip: now hard-clip arguments do differently for r1 and r2. This change is adjusted for metabarcoding data. Remove -C --clip-after -c --clip5; add -b --clip-after-r1 -B --clip-after-r2 -e --clip5-r1 -E --clip5-r2.
• Optimize: --detect-adapter for paired-end reads now guess adapters from pair information, rather than the existing adapter pool.
• Feature: users can customize order of processing: -O | --order.
• Doc: installation from source: using juliaup to select julia version 1.8.5. Atria runs faster when using 1.8.5 rather than 1.9.3.

Full Changelog: v3.2.2...v4.0.0

v3.2.2-1

• Fix: When running atria v3.2.2 with switch --stats, encounter error not seen in v3.2.1 (#13, thanks to @kalavattam)

Full Changelog: v3.2.2...v3.2.2-1

v3.2.2

• Optimize: speed up for threads <= 2.
• Fix: atria test should not depend on source files.
• Julia version 1.8.5.

v3.2.1

• Atria skips completed analysis by default.

v3.2.0-dev

• Remove multi-proc mode since it is unstable.
• Logging: new logging for versions and sample completion.
• Fix v3.1.3: multi-proc mode: Julia v1.8.1 does not allow assign new ARGS, and add -t nthread in julia_args.
• Fix v3.1.3: pe-consensus: error when insert_size = -1; fix trimming when insert_size = -1.
• Benchmark iscomplement in Atria v3.1.2 and that in BioSequences, and found it is good to stick to BioSequences.

v3.1.2

Fix: optimize output file names if ending with .bz2.