Yacrd Versions Save

Change:

• Replace rust-bio by noodles
• Bump to stable Clap 3

Some change:

• Don't crash, when yacrd report parser see a perfect read
• Replace structopt by clap-3.0.0-beta

Just some small change:

• Avoid crash when paf record have different number of SAM like optional file
• Update dependency
• Use niffler release version

Compatibility with previous version is broken, again yes I'm sorry but this is the last time

Change:

• all post-detection operation (extract, filter, split, scrubb) are now subcommand
• chimeric-threshold option is renamed coverage
• not-covered-threshold option is renamed not-coverage
• memory usage is reduced but the length of read need to be lower than 2^32
• add an ondisk mode to reduce again the memory usage, on this mode memory usage is linear in the number of read, in basic mode memory usage is linear in the number of overlap
• more understandable error messages

Thanks to Peter Ebert (for the idea of disk mode), Luiz Iber (for niffler, and discovering of many useful crates), and all people they found bug in development and previous version.

It's probably the last version before 1.0

Break compatibility with previous version.

Add two subcommand:

• chimeric: behavior of the previous version
• scrubbing: removes all unsupported read fragments

Bug correction:

• MHAP shared min-mers can be float
• correct error in help message

New Feature:

• yacrd can write report in json if flag -j or --json are set

New PostDetection operation:

• extract : write in name_extracted.{paf|mhap|fasta|fastq} Chimeric and Not_covered read
• spilt: write in name_spilt.{fasta|fastq} part of read with sufficient coverage

Bug correction:

• In PostDetection output name generation in fliterd input is ../something.other/test.fasta output are ../something.other/test_filtred.fasta not ._filtred./something.other/test.fasta

Complete rewrite in Rust.

Change log:

• Support of compressed file
• Read from stdin
• Add unit and functional test

Changelog:

• Solve compilation error on gcc-5
• Add version option

First yacrd release !

yacrd take long read mapping tools result (minimap, mhap, graphmap) and find chimeric long-read.