v4.1.4

• Change: compressed file: better infer inbyte size when file does not output actual original file size.

v4.1.3

• Fix: when the paired end files are compressed, read chunks did not resize, which led to excessive copy, and copy number might accumulate round by round.

v4.1.2

• Fix: do not throw error if input paired end files are empty when doing --detect-adapter.

v4.1.1-1

• Fix: MaxOS build script: cannot copy dylibs.

v4.1.1

Fix: -z NUM -Z NUM error when length to trim < 0.

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