obitools4/Release-notes.md

OBITools release notes

On going changes

Corrected bugs

• Makes progress bar updating at most 10 times per second.
• Makes the command exiting on error if undefined options are used.

New features

• Takes into account the OBIMAXCPU environmental variable to limit the number of CPU cores used by OBITools in bash the below command will limit to 4 cores the usage of OBITools

  export OBICPUMAX=4
  

• Adds a new option --out|-o allowing to specify the name of an outpout file.

  obiconvert -o xyz.fasta xxx.fastq
  

  is thus equivalent to

  obiconvert  xxx.fastq > xyz.fasta
  

  That option is actually mainly useful for dealing with paired reads sequence files.

• Some OBITools (now obigrep and obiconvert) are capable of using paired read files. Options have been added for this (--paired-with FILENAME, and --paired-mode forward|reverse|and|andnot|xor). This, in combination with the --out option shown above, ensures that the two matched files remain consistent when processed.

February 18th, 2023. Release 4.0.0

It is the first version of the OBITools version 4. I decided to tag then following two weeks of intensive data analysis with them allowing to discover many small bugs present in the previous non-official version. Obviously other bugs are certainly persent in the code, and you are welcome to use the git ticket system to mention them. But they seems to produce now reliable results.

Corrected bugs

• On some computers the end of the output file was lost, leading to the loose of sequences and to the production of incorrect file because of the last sequence record, sometime truncated in its middle. This was only occurring when more than a single CPU was used. It was affecting every obitools.
• The obiparing software had a bug in the right aligment procedure. This led to the non alignment of very sort barcode during the paring of the forward and reverse reads.
• The obipairing tools had a non deterministic comportment when aligning a paor very low quality reads. This induced that the result of the same low quality read pair was not the same from run to run.

New features

• Adding of a --compress|-Z option to every obitools allowing to produce gz compressed output. OBITools were already able to deal with gziped input files transparently. They can now produce their résults in the same format.
• Adding of a --append|-A option to the obidistribute tool. It allows to append the result of an obidistribute execution to preexisting files.
• Adding of a --directory|-d option to the obidistribute tool. It allows to declare a secondary classification key over the one defined by the '--category|-c` option. This extra key leads to produce directories in which files produced according to the primary criterion are stored.
• Adding of the functions subspc, printf, int, numeric, and bool to the expression language.