The current bin folder contains a lot of scripts that are not mean for user-compsumption and should be removed or moved to a different package.
[ ] *_mapping.pl: perl scripts for mapping. This scripts should be moved to libexec or lib (accessible for distmap, but not for the user). In addition, it is preferable to prefix them with distmap- to recognize that they belong to distmap.
[ ] exonerate.sh: is this used anywhere? Otherwise, this script is for a mapper and should have the same fate as the previous one.
[ ] read-fasta.pl: used in exonerate.sh - should be the same as before.
[ ] cluster_trimming.pl: this should be removed, as trimming on the cluster is deprecated.
[ ] dowload_merge_fastq.pl: this should be removed, as downloading merged FASTQ is deprecated
[x] filter_reads.py: unused and not really needed in the software.
The current bin folder contains a lot of scripts that are not mean for user-compsumption and should be removed or moved to a different package.
*_mapping.pl: perl scripts for mapping. This scripts should be moved tolibexecorlib(accessible for distmap, but not for the user). In addition, it is preferable to prefix them withdistmap-to recognize that they belong to distmap.exonerate.sh: is this used anywhere? Otherwise, this script is for a mapper and should have the same fate as the previous one.read-fasta.pl: used inexonerate.sh- should be the same as before.cluster_trimming.pl: this should be removed, as trimming on the cluster is deprecated.dowload_merge_fastq.pl: this should be removed, as downloading merged FASTQ is deprecatedfilter_reads.py: unused and not really needed in the software.