Describe the bug
If we provides a FASTA file instead of a FASTQ file to MATAM, the contigs assembly step does not work as expected.
The extract_reads_by_component function is expecting a FASTQ file and reads the file a such.
To Reproduce
Run MATAM in default mode with a FASTA (converting the FASTQ file of the example to a FASTA will be sufficient).
We have to remove the possibility to use a FASTA file as input.
Describe the bug If we provides a FASTA file instead of a FASTQ file to MATAM, the contigs assembly step does not work as expected. The extract_reads_by_component function is expecting a FASTQ file and reads the file a such.
To Reproduce Run MATAM in default mode with a FASTA (converting the FASTQ file of the example to a FASTA will be sufficient).
We have to remove the possibility to use a FASTA file as input.