Bug: @remove directive not parsed correctly in config file

[bentyeh]

Since its introduction in version 0.29.4 (and through the current version 0.31.2), the @remove directive in the config file has not been parsed correctly, even though instructing splitcode to perform the same remove operation via the -r/--remove command line argument works correctly.

Minimum working example

• input.fastq

  @read1
  AAA
  +
  ;;;
  

• config.txt

  id	tag
  tag1	AAA
  

• config_with_remove.txt

  @remove:
  tag1
  
  id	tag
  tag1	AAA
  

The command

splitcode -c config.txt --mod-names --out-fasta --nFastqs=1 -o /dev/stdout input.fastq

correctly identifies tag1

>read1::[tag1]
AAA

and adding a remove directive via the command line works as expected:

splitcode -c config.txt --mod-names --remove=<(echo "tag1") --out-fasta --nFastqs=1 -o /dev/stdout input.fastq

generates empty output. However,

splitcode -c config_with_remove.txt --mod-names --remove=<(echo "tag1") --out-fasta --nFastqs=1 -o /dev/stdout input.fastq

produces a standard output of

>read1::[tag1]
AAA

and a standard error of

Name "tag1 " does not exist
* Using a list of 1 tags (vector size: 1; map size: 1; num elements in map: 1)
* will process sample 1: input.fastq
* processing the reads ...
done 
* processed 1 reads

See also https://colab.research.google.com/drive/1NGGEudqUrxdYBtgyeBS0APOVzIo84kcX for an executable example.

[Yenaled]

fixed